BioCyc Glossary

Index

A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z
0-Centered Scale, Omics Viewer
0-centered scale: implies that the numerical data of the Omics Viewer data file can contain positive and negative values. The value 0 is considered to be the center of the numerical values provided in the data file.
1-Centered Scale, Omics Viewer
1-centered scale: implies that any negative or zero values in the data file should be skipped. Moreover, the data is centered around the value 1 using a log scale. For example, the value 0.1 is considered to be at the same distance to 1 as the value 10. So, a logarithm of base 10 is applied to the data before the linear coloring mapping is applied.
3' (3-prime)
A term that identifies one end of a single-stranded nucleic acid molecule. The 3' end is that end of the molecule which terminates in a 3' phosphate group. The 3' direction is the direction toward the 3' end. Nucleic acid sequences are written with the 5' end to the left and the 3' end to the right, in reference to the direction of DNA synthesis during replication (from 5' to 3'), RNA synthesis during transcription (from 5' to 3'), and the reading of mRNA sequence (from 5' to 3') during translation. See the Figure at NHGRI.
See also:
3' UTR
3' Untranslated Region. That portion of an mRNA from the 3' end to the position of the last codon used in translation.
See also 5' UTR.
5' (5-prime)
A term that identifies one end of a single-stranded nucleic acid molecule. The 5' end is that end of the molecule which terminates in a 5' phosphate group. The 5' direction is the direction toward the 5' end. Nucleic acid sequences are written with the 5' end to the left and the 3' end to the right, in reference to the direction of DNA synthesis during replication (from 5' to 3'), RNA synthesis during transcription (from 5' to 3'), and the reading of mRNA sequence (from 5' to 3') during translation. See the Figure at NHGRI.
See also:
5' UTR
5' Untranslated Region. That portion of an mRNA from the 5' end to the position of the first codon used in translation.
See also 3' UTR.
Ab initio
Formulated without experimental data. Latin. From the beginning.
Absolute Data Values, Omics Viewer
The numerical values in the data file that are positive only, no negative values are included.
Accession ID
A unique alphanumeric character string that is used to unambiguously identify a particular record in a database. Examples include MGI accession IDs, GenBank accession IDs, and PubMed accession IDs.
Adenine (A)
A purine base that is a component of nucleotides and thus a normal component of DNA and RNA. See the Figure at NHGRI.
Algorithm
A detailed sequence of actions to perform to accomplish some task. Technically, an algorithm must reach a result after a finite number of steps, thus ruling out brute force search methods for certain problems, though some might claim that brute force search was also a valid (generic) algorithm. The term is also used loosely for any sequence of actions (which may or may not terminate).
Alias
In MGI, an alternative symbol or name for part of the sequence of a known gene that resembles names for other anonymous DNA segments. For example, D6Mit236 is an alias for Cftr.
Allele
One of the variant forms of a gene, differing from other forms in its nucleotide sequence.
Allele Pair
A designation of the specific alleles present on the two homologous chromosomes for a given locus.
Alternative Splicing
The production of two or more distinct mRNAs from RNA transcripts having the same sequence via differences in splicing (by the choice of different exons).
Amino Acid
A molecule of the general formula NH2-CHR-COOH, where "R" is one of a number of different side chains. Amino acids are the building blocks of proteins. The sixty-four codons of the genetic code allow the use of twenty different amino acids (the primary amino acids) in the synthesis of proteins. Other nonprimary amino acids occur in proteins by enzymatic modification of amino acids in mature proteins, and as metabolic intermediates. See the Figure at NHGRI. For Figures showing the structure of each of the twenty primary amino acids, see Figure 1 and Figure 2 from "Molecular Biology of the Cell" by Alberts et al. at Access Excellence.
Amino Terminus
A term that identifies one end of a protein molecule. The amino terminus is that end of the molecule which terminates in a free amino group. See the Figure at NHGRI.
See also:
Amplification
An increase in the number of copies of a specific DNA fragment; can be in vivo or in vitro.
See also PCR (polymerase chain reaction).
Ancestor
In MGI, this term refers to terms in a hierarchical controlled vocabulary such as those containing Gene Ontology (GO), Mammalian Phenotype Ontology, and Adult Mouse Anatomical Dictionary terms. An "ancestor" of a term is a term any number of levels above it in the hierarchy from which it is descended. For example, the GO term enzyme [GO:0003824] is an ancestor to the GO term alcohol dehydrogenase [GO:0004022].
See also:
Aneuploid
Not euploid.
Annotation
1. n. Database entries that provide supplementary information about a biological entity, such as annotation of pathways or regulatory sites.
2. v. The analysis process used to create annotations.
See also Sequence Annotation.
Anonymous DNA segment
A segment of DNA not known to correspond to a named gene that can be used as a marker in the construction of genetic maps.
See also STS.
ANSI
American National Standards Institute. ANSI is a private, non-profit organization that administers and coordinates the U.S. voluntary standardization and conformity assessment system. The Institute's mission is to enhance both the global competitiveness of U.S. business and the U.S. quality of life by promoting and facilitating voluntary consensus standards and conformity assessment systems, and safeguarding their integrity. For further information, see the web site for ANSI.
Antibody
A protein produced by cells of the immune system that binds to an antigen. See the Figure at NHGRI.
See also Monoclonal Antibody.
Antigen
A protein or other molecule that can elicit an immune response; the antibody protein that is produced binds to the antigen.
Antimorphic Mutation
A type of mutation in which the altered gene product possesses an altered molecular function that acts antagonistically to the wild-type allele. Antimorphic mutations are always dominant or semidominant.
See also:
Antisense
  1. In molecular biology, that strand of a DNA molecule whose sequence is complementary to the strand represented in mRNA.
  2. In molecular biology, an RNA molecule complementary to the strand normally processed into mRNA and translated.
Apoptosis
Programmed cell death, that is, the death of cells by a specific sequence of events triggered in the course of normal development (e.g., cells between digits in the limb bud) or as a means of preserving normal function (e.g., in response to viral infection).
Arrayed Library
Individual primary recombinant clones (hosted in phage, cosmid, YAC, or other vector) that are placed in two-dimensional arrays in microtiter dishes. Each primary clone can be identified by the identity of the plate and the clone location (row and column) on that plate. Information gathered on individual clones from various experimental techniques is entered into a relational database and used to construct physical and genetic linkage maps simultaneously; clone identifiers serve to interrelate the multilevel maps.
See also library.
ASCII
American Standard Code for Information Interchange. The basis of character sets used in almost all present-day computers.
Assay
In general, the qualitative or quantitative analysis of a substance. In MGI, an assay is a type of experiment that is designed to detect the level of gene expression of a particular gene, or to determine the pattern of expression of a gene among different tissue types, anatomical structures, or developmental stages. The assay may detect one or more of the RNA transcripts of a gene or one or more of its protein products. Assay types in MGI include:
Assembly Coordinates
Numerical values defining a sequence interval along a chromosome in the mouse genome assembly. In MGI, gene sequences are defined as the interval between the start position of the first exon and the end position of the last exon of a gene as annotated by NCBI Gene or Ensembl. See NCBI Gene Model and Ensembl Gene Model for further information.
Assembly Sequence
The sequence defined by an interval along a chromosome in the mouse genome assembly. In MGI, assembly sequences are defined as the interval between the start position of the first exon and the end position of the last exon of a gene as annotated by the NCBI or Ensembl gene models. See NCBI Gene Model and Ensembl Gene Model for further information.
ATCC
American Type Culture Collection. A large collection of microbial stocks, including microbes containing mammalian DNA segments. See the ATCC Home Page for further information.
Attribute
A property inherent in an entity or associated with that entity for the purpose of managing a database.
Autoradiography
The detection of a unstable isotope that emits radiation by a photographic emulsion. In the case of in situ hybridization, this involves dipping microscope slides in liquid emulsion. In the case of Southern blots, Northern blots, or Western blots, the membrane is placed next to a sheet of X-ray film.
Autosome
Any chromosome that is not a sex chromosome.
BAC
Bacterial Artificial Chromosome. A type of cloning vector derived from the naturally-occurring F factor episome. A BAC can carry 100 - 200 kb of foreign DNA.
Backcross
A type of cross in which a hybrid strain is crossed to one of the two parental strains.
See also:
Bacteriophage
A virus that infects bacteria.
BAC/YAC End
BAC/YAC end refers to sequences at the end of foreign DNA inserts in a BAC or YAC. These sequences are a source of STSs to determine the extent of overlap between BACs or YACs and to aid in the alignment of sequence contigs.
Base
One of a set of nitrogenous compounds attached to the sugar-phosphate backbone in a nucleic acid. In DNA, the purine bases are adenine (A) and guanine (G), while the pyrimidine bases are cytosine (C) and thymine (T). In RNA, the purine bases are adenine (A) and guanine (G), while the pyrimidine bases are cytosine (C) and uracil(U). See the Figure at NHGRI.
Base Pair
In double-stranded nucleic acids, a "base pair" is the structure formed between two complementary nucleotides by hydrogen bonding. In DNA, adenine(A) pairs with thymine (T) and cytosine (C) pairs with guanine (G). In RNA, adenine (A) pairs with uracil (U) and cytosine (C) pairs with guanine (G). See the Figure at Access Excellence.
Base Pathway
Base pathways describe pathways that are not composed of other, smaller pathway (i.e., that are not super-pathways).
Base Sequence
The order of nucleotide bases in a DNA or RNA molecule.
Binding-Reactions
This Pathway Tools ontology class consists of reactions in which no covalent modification of the substrates takes place, but in which the net effect is that one substrate noncovalently binds to or unbinds from another molecule via weak bonds (e.g. hydrogen bonds).
BioCyc
BioCyc is a collection of hundreds of Pathway/Genome Databases at URL BioCyc.org created by the group of Dr. Peter D. Karp at SRI International. BioCyc includes two very highly curated PGDBs: MetaCyc, a PGDB containing more than 1,200 experimentally elucidated metabolic pathways from more than 1,500 organisms, and EcoCyc, a PGDB for Eschericahia coli K-12.
Bioenergy Pathways
These pathways are primarily involved in biomass conversion and biofuels production.
Bioinformatics
The application of computer technology to the management of biological information. Specifically, it is the science of developing computer databases and algorithms to facilitate and expedite biological research, particularly in genomics.
Biological Process
Refers to a broad category of biological tasks accomplished via one or more ordered assemblies of molecular functions. Usually there is some temporal aspect to it, although a process event may be essentially instantaneous. It often involves transformation, in the sense that something goes into a process and something different comes out of it. Examples of biological processes included in this category are cell growth and maintenance, signal transduction, pyrimidine metabolism, and cAMP biosynthesis. In the GO Project vocabularies, Biological Process is a primary class of terms. See the GO Consortium site for further information.
BioPAX
BioPAX is an OWL RDF/XML-based format for exchange of pathway data.
Biosynthesis
Synthesis of chemical compounds by enzymatic processes in living organisms.
Biotin
One of the water-soluble B vitamins. It is useful in molecular biology as a chemical tag on nucleic acid probes or antibodies, because the biotin-scavenging proteins avidin and streptavidin bind biotin with high affinity. These biotin-binding proteins can be coupled to fluorescent dyes, enzymes that can be detected using chromogenic reactions, or colloidal gold, allowing detection of biotin-labeled probes or antibodies on Southern blots, Northern blots, Western blots, or cytological preparations.
BioVelo
BioVelo is a concise query language that has been developed to query biological databases created with Pathway Tools. BioVelo is based on a simple mathematical concept (list comprehension) and is simpler than the concepts used by SQL (Structured Query Language).
BLAST
Basic Local Alignment and Searching Tool. A sequence comparison algorithm optimized for speed used to search sequence databases for optimal local alignments to a query sequence. There is a description of the specific algorithm used, and additional information, at NCBI.
Boolean
Refers to an expression that must evaluate to a value of true or false, named for the British mathematician George Boole. In MGI and other databases, Boolean refers to the kind of logical relationship among search terms. Boolean operators include AND, OR, and NOT. For example, searching for all markers of the type "Gene" on Chromosome 2 is equivalent to identifying the union of the two sets:
  1. all markers of the type "Gene" (Type Gene?=true) AND
  2. all markers on Chromosome 2 (Chromosome 2=true).
Build
In NCBI, the end result of processes used to assemble genomic sequence data, annotate features, and provide a dataset of assembled genomic sequence, RNAs, and proteins. Such processes are complex; NCBI continues to refine them so that regions not fully represented will improve with subsequent builds.
See also: assembly sequence.
cAMP
Cyclic AMP. A form of the nucleotide adenosine monophosphate that serves as a signaling molecule within and between cells.
Carboxyl Terminus
A term that identifies one end of a protein molecule. The carboxyl terminus is that end of the molecule which terminates in a free carboxyl group. See the Figure at NHGRI.
See also:
Catabolism
Degradation of chemical compounds into compounds having a lower molecular weight by enzymatic processes in living organisms.
cDNA
Complementary DNA. A DNA copy of an mRNA or complex sample of mRNAs, made using reverse transcriptase.
Cellular Component
Refers to subcellular structures, locations, and macromolecular complexes. Some examples are nucleus, telomere and origin recognition complex. In the GO Project vocabularies, Cellular Component is a primary class of terms. See the GO Consortium site for further information.
Cellular Overview
The Cellular Overview diagram is a representation of all metabolic pathways and reactions, signaling pathways, membrane proteins, and transporters defined for the current organism.
Centimorgan
A unit of length in a genetic map. Two loci are 1 cM apart if recombination is detected between them in 1% of meioses.
Central Dogma
The principal statement of the molecular basis of inheritance. In its simplest form:

"DNA makes RNA makes protein."

This means that (generally) genetic information is stored in and transmitted as DNA. Genes are expressed by being copied as RNA (transcription), which is processed into mRNA via splicing and polyadenylation. The information in mRNA is translated into a protein sequence using a genetic code to interpret three-base codons as instructions to add one of twenty amino acids or to stop translation. See the Figure at Access Excellence or the Figure at NHGRI.
Centromere
In mammalian genetics, the primary constriction of a chromosome separating it into the short arm (p) and the long arm (q). The centromere is the chromosomal region over which the kinetochore is organized. See the Figure at NHGRI. Mouse chromosomes have centromeres close to one end and have essentially no short arm. See the idiogram of the mouse karyotype at the Department of Pathology at the University of Washington.
Chemically Induced Mutation
A mutation induced by treatment with a chemical mutagen, for example, ENU (ethyl nitrosourea) or chlorambucil.
Chemical-Reactions
This Pathway Tools ontology class defines reactions for which at least one substrate molecule is chemically modified, meaning that either a chemical bond (covalent, ionic or coordination) is formed and/or broken, or that a redox modification has occurred.
Chiasma
The cytologically visible consequence of a reciprocal recombination event in meiosis, observable in the later stage of meiotic prophase. Chiasmata hold homologous chromosomes together prior to anaphase of the first meiotic division.
Children
In MGI, this term refers to terms in a hierarchical controlled vocabulary like ones containing Gene Ontology (GO) terms. A "child" of a term is a term any number of levels below it in the hierarchy that is a descendant of the term. For example, the GO term alcohol dehydrogenase [GO:0004022] is a child of the GO term enzyme [GO:0003824].
See also:
Chimera
  1. An animal formed from two different animals, that is from two different embryonic sources. In mouse genetics, targeted mutations produced in embryonic stem cells are recovered by breeding chimeric mice resulting from the mixture of ES cells with a genetically-distinct blastocyst.
  2. A clone containing genomic DNA from nonadjacent genomic segments or cDNA from two different mRNAs.
    See also Cloning Artifact.
Chimeric Pathways
A chimeric pathway comprises reactions from multiple organisms, and most commonly does not occur in its entirety in a single organism. Chimeric pathways are always superpathways. Chimeric pathways are intended to depict a set of related pathways across multiple organisms.
Choke Point Reaction Finder
Choke-point reaction finder is a tool to find choke point reactions in a PGDB.
Choke-Point Reactions
A chokepoint reaction is a reaction that either uniquely consumes a specific reactant or uniquely produces a specific product in a metabolic network.
Chromatin
The nuclear material that makes up chromosomes, consisting of DNA and protein.
See also:
Chromogenic
Color-generating. A chromogenic substrate is colorless until acted upon by an enzyme; it then becomes an insoluble pigment.
Chromosome
A structural unit within a eukaryotic nucleus that carries genes. A chromosome consists of a long, continuous strand of DNA and associated proteins. See the Figure at NHGRI.
Chromosome Aberration
  1. A chromosome rearrangement.
  2. Less commonly, a numerical aberration.
Chromosome Rearrangement
A kind of mutation in which there is a change in the arrangement of the genome into chromosomes; this term usually applies to those changes that are visible cytogenetically.
Classes of chromosome rearrangements include:
Clone
  1. A segment of DNA contained within a cloning vector.
  2. An organism derived from a founding individual by asexual means that is genetically identical to the founding individual.
Cloning Artifact
A DNA clone whose structure does not accurately represent genomic or mRNA sequence, due to errors in the cloning process. For example, two noncontiguous genomic fragments may be joined by ligation prior to being incorporated into the cloning vector.
Cloning Vector
A DNA construct capable of replication within a bacterial or yeast host that can harbor foreign DNA, facilitating experimental manipulation of that DNA segment.
cM
See centimorgan.
Coding Region
That part of a gene whose sequence is read as codons during translation.
See also:
Codominant
One of a series of terms applied to the phenotypic effect of a particular allele in reference to another allele (usually the standard wild-type allele) with respect to a given trait. An allele "a" is said to be codominant with respect to the wild-type allele "A" if the A/a heterozygote fully expresses both of the phenotypes associated with the a/a and A/A homozygotes. An example of codominance is the ABO blood type antigens in humans, where AA individuals are type A, BB individuals are type B, and AB individuals are type AB.
See also:
Codon
Three bases in a DNA or RNA sequence that specify an amino acid or a termination signal (stop codon). See the Figure at Access Excellence.
See also:
Colloidal Gold
Fine particles of gold (on the order of 5-20 nm diameter) that can be coupled to antibodies or other proteins, allowing the detection of the binding of the labeled proteins by electron microscopy.
Complementary DNA
See cDNA.
Common name
A common name is the name that is used in BioCyc to refer to an object. In many cases, a single object may have many synonyms, but only one of those can be designated a common name.
Complementary Sequence
A single-stranded nucleic acid that would bind to a given single-stranded nucleic acid by following base pairing rules (A pairs with T and C with G). The complementary sequence to GTAC for example, is CATG.
Complementation
The appearance of a wild-type phenotype in an individual that is the hybrid offspring of two mutant individuals homozygous for recessive mutations. Complementation shows that the two parental mutant individuals have mutant alleles of different genes, even if they are phenotypically similar. For example, a cross between two light gray mice(ash/ash and d/d) would produce a black mouse.
Complex/Cluster/Region
In MGI, the marker type "Complex/Cluster/Region" refers to any of the following:
  1. Gene complex; a group of genes closely linked together that are related evolutionarily or functionally. Interspersed unrelated genes located within the group are included.
  2. A segment of the mouse genome defined by comparison to an orthologous segment in the genome of another species, or by some specific characteristic, such as loss of heterozygosity.
  3. A marker repository for information pertaining to a specific gene family, where such information lacks precise family member resolution.
Compound Heterozygote
A heterozygote where different mutant alleles are present at the two copies of a given locus. In MGI, a compound heterozygote occurs when the two opposing alleles are associated with different MGI markers.
Conditional Genotype
A genotype that is dependent on the presence of some other factor (often a DNA sequence that expresses a protein functioning in specific recombination events). In MGI, conditional is most commonly used to represent Cre-mediated excision of genomic sequences flanked by loxP sites. In most instances, excision of the endogenous genomic sequence flanked by loxP sites is accompanied by simultaneous insertion of some selectable marker (e.g. neomycin). The excised genotype, which is often associated with a phenotype, is dependent (or conditional) on the presence of the Cre-expressing construct.
Conserved Sequence
A base sequence in a DNA molecule (or an amino acid sequence in a protein) that has remained relatively unchanged throughout evolution.
Conserved Synteny
The occurrence of synteny of orthologous genes in two different organisms. Conserved synteny between mouse and human does not usually extend over entire chromosomes, with the exception of the X chromosome. See the Orthology Map for a graphical display of conserved synteny.
Consistency Checker
The Pathway Tools Consistency Checker corrects some data correctness violations in PGDBs, and flags other violations for manual review by the user.
Conspecific Pathways
A conspecific pathway comprises a set of reactions that are expected to be found within each organism that has the pathway. Conspecific pathways can be either base pathways or superpathways.
Contig
  1. A physical map of contiguous genomic DNA assembled using overlapping cloned segments (see STS).
  2. A contiguous DNA sequence assembled using overlapping DNA sequences.
Controlled Vocabulary
A restricted set of defined terms allowing the representation of complex information in a database. See Gene Ontology, Mammalian Phenotype Ontology, and Adult Mouse Anatomical Dictionary terms.
Cosmid
A type of cloning vector derived from bacteriophage lambda. A cosmid can carry about 40 kb of foreign DNA.
Cre Recombinase
A site-specific recombination enzyme that recognizes the 34 base pair loxP sequence.
Cross
An experimental mating of two genetically distinct sexually reproducing organisms.
See also:
Cross-hybridization
With respect to nucleic acids, "cross-hybridization" refers to the formation of double-stranded DNA, RNA, or DNA/RNA hybrids by complementary base pairing between two molecules that are not identical in sequence. Cross-hybridization may be observed between nucleic acids derived from orthologous or paralogous genes.
Crossover
A reciprocal recombination event.
Cryopreservation
The process by which living cells, organs, or organisms are frozen and maintained with the intent to revive them as functional units in the future.
Cy5
A fluorescent dye used to label DNA probes for FISH or antibodies for immunofluorescence or Western blots.
Cytoband
See Cytogenetic Band.
Curator
A person who performs curation on a database. See Curation.
Curation
The process of manually updating and refining a bioinformatics database. Literature-based curation involves updates database based on information found in the scientific literature. Curation involves updating both structured database fields, and English text such as mini-review summaries that capture information not captured by the highly structured sections of the database. For example, curators may use the free-text comment sections to capture information such as similarity to other proteins or data from functional complementation experiments. The comment section is also to be used to note cases in which the published reports present contradictory results. In such cases, both viewpoints will be presented with proper attribution. This approach assures that no information is lost.
Cytogenetic
Refers to the correlation of genetic and cytological information through the microscopic analysis of stained preparations of chromosomes, including those from individuals carrying mutations.
Cytogenetic Band
One of the subregions of a chromosome visible microscopically after special staining.
Cytogenetic Map
A type of genetic map relating gene positions to chromosomal banding patterns. The maps are built from relating the positions of genes to cytogenetic markers or by in situ hybridization.
See also:
Cytogenetic Marker
  1. A structure within a chromosome that is visible by microscopic examination, possibly after special staining methods are used.
  2. A chromosome rearrangement that is visible by microscopic examination.
Cytoplasm
That part of a eukaryotic cell that is not the nucleus.
Cytosine (C)
A pyrimidine base that is a component of nucleotides and thus a normal component of DNA and RNA. See the Figure at NHGRI.
DAG
Directed Acyclic Graph. See Dictionary of Algorithms and Data Structures.
Database
A data structure that stores metadata, i.e. data about data. More generally, an organized collection of information.
Database Management System (DBMS)
A collection of computer programs that allow storage, modification, and extraction of information from a database. There are many different types of DBMSs, ranging from small systems that run on personal computers to huge systems that run on mainframes. The following are examples of database applications:
  • computerized library systems
  • automated teller machines
  • flight reservation systems
  • computerized parts inventory systems
  • MGI
Data dictionary
In computer science, a table in a database that stores the names, field types, length, and other characteristics of the fields in the database tables.
DBMS
Database Management System.
See also Database Management System.
Dead End Metabolite
Dead-end metabolites are those that are either only consumed, or only produced, by the reactions within a given cellular compartment, including transport reactions.
Default
In MGI and in computer science in general, a setting or action assumed by a computer program when none is specified by the user.
Degenerate
A term describing one of the qualities of the genetic code, specifically, that some amino acids may be specified by more than one codon.
Deletion
A type of mutation caused by loss of one or more nucleotides from a DNA segment. Deletions can be very large, encompassing many genes and megabases of DNA, to the point of producing a visible cytological abnormality in a chromosome. Small deletions within a gene can alter the reading frame, and thus the amino acid sequence of the encoded protein. See the Figure at NHGRI.
Denaturation
  1. The separation of the two strands of a double-stranded nucleic acid caused by treatments that overcome hydrogen bonding, e.g., heat.
  2. A usually irreversible change in the conformation of a protein caused by treatments that overcome hydrogen bonding, hydrophobic interactions, or other chemical forces that maintain the structure of proteins, e.g., heat.
Deoxyribonucleotide
A monomer unit of DNA, consisting of a purine or pyrimidine base, a deoxyribose sugar molecule, and phosphate group(s).
Dimorphic
Having two forms.
Diploid
Having twice the chromosome number normally found in a gamete. Normal mice are diploid, having a chromosome set from the maternal gamete (the egg) and a chromosome set from the paternal gamete (the sperm).
See also Haploid.
Direct detection
Indicates that the expression of the reporter gene was detected using a direct method, such as fluorescence or using an enzymatic substrate.
Directed Acyclic Graph (DAG)
A directed graph where no path starts and ends at the same vertex. See Dictionary of Algorithms and Data Structures.
Directed Sequencing
The sequencing of a large DNA segment through the sequencing of subsegments known to be adjacent.
See also Shotgun Sequencing.
DNA
Deoxyribonucleic acid. The nucleic acid of which genes are made. See the Figure at NHGRI.
See also:
DNA Construct
An assembly of DNA sequences made in vitro to serve an experimental purpose.
DNA Mapping Panel
A data set obtained by DNA typing of polymorphic markers in backcrosses of hybrid organisms.
DNA Methylation
Attachment of methyl groups (-CH3) to DNA, most commonly at the cytosine bases.
DNA Polymerase
An enzyme that carries out replication.
DNA Replication
The use of existing DNA as a template for the synthesis of new DNA strands. In eukaryotes, replication occurs in the cell nucleus.
DNA Segment
  1. A length of DNA.
  2. A DNA segment is a genomic feature recognized by anonymous DNA probes. Symbols for such segments most commonly represent intergenic markers used in genetic mapping.
DNA Sequence
The relative order of base pairs, whether in a fragment of DNA, a gene, a chromosome, or an entire genome.
dNTP
Deoxyribonucleotide triphosphate. A generic term referring to the four deoxyribonucleotides: dATP, dCTP, dGTP and dTTP. See the Figure at NHGRI.
Dominant
One of a series of terms applied to the phenotypic effect of a particular allele in reference to another allele (usually the standard wild-type allele) with respect to a given trait. An allele "A" is said to be dominant with respect to the allele "a" if the A/A homozygote and the A/a heterozygote are phenotypically identical and different from the a/a homozygote.
See also:
DoTS
Database of Transcribed Sequences. The DoTS human and mouse transcript index is created from all publicly available transcript sequences. Input sequences are clustered and assembled to form the DoTS Consensus Transcripts that make up the index.
Double Helix
The shape that two linear strands of DNA assume when hydrogen-bonded together.
Draft Genome Sequence
Sequence of genomic DNA having lower accuracy than finished sequence; some segments are missing or in the wrong order or orientation.
See also Finished Sequence.
Duplication
An additional copy of a DNA segment present in the genome. Gene duplication is the source of paralogous genes. See the Figure at NHGRI.
EC Number
A number assigned to a type of enzyme according to a scheme of standardized enzyme nomenclature developed by the Enzyme Commission of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB). EC numbers may be found in ENZYME, the Enzyme nomenclature database, maintained at the ExPASy molecular biology server of the Geneva University Hospital and the University of Geneva, Switzerland.
EcoCyc
A Pathway/Genome Database describing the genome, metabolic network, and regulatory network of Escherichia coli K-12. Available at URL EcoCyc.org. EcoCyc is a member of the BioCyc Database Collection.
Escherichia coli
Common bacterium that geneticists have studied intensively because of its small genome size, normal lack of pathogenicity, and ease of growth in the laboratory.
Electrophoresis
The separation of charged molecules (DNA, RNA or protein) in an electrical field, usually in a supporting medium such as an agarose or polyacrylamide gel.
Electroporation
The use of strong, brief pulses of electric current to create temporary holes in cell membranes, allowing the introduction of DNA.
Endogenous
Contained within. In genetics, endogenous viruses are those that are integrated into the genome and transmitted to progeny as chromosomal elements.
Endonuclease
A protein that cleaves the phosphodiester backbone of a nucleic acid enzymatically, for example a restriction enzyme.
Engineered Pathways
Such pathways do not occur naturally in any known organism, and have been constructed in a living cell by metabolic engineering.
Enhancer
One of the necessary regulatory elements of a gene. An enhancer is a site on DNA to which a complex of transcription factors binds to affect the availability of the promoter to RNA polymerase. A gene may have multiple enhancers.
Enhancer Trap
A type of DNA construct containing a reporter gene sequence downstream of a promoter that is capable of integrating into random chromosomal locations. Integration of the enhancer trap near an enhancer allows the expression of a new mRNA encoding the reporter gene. The reporter gene is therefore expressed in the cells and developmental stages where the enhancer is active.
See also Gene Trap.
Enrichment Analysis
Enrichment analysis aids in determining whether a set of entities is statistically over-represented for another set of entities of interest. For example, is a set of genes enriched in known metabolic pathways or Gene Ontology terms? Is a set of metabolites enriched for known metabolic pathways? Enrichment analysis can identify phenomena underlying gene-expression data, for example.
Ensembl Gene Model
A description of a gene associated with a genome assembly from a genome sequencing project. The gene model includes the coordinates of each intron and exon, as well as the beginning and end of the transcript.
Enzymatic Reactions
Frames in the class Enzymatic-Reactions describe attributes of an enzyme with respect to a particular reaction that it catalyzes.
Enzyme
A protein (or rarely, RNA) that catalyzes a chemical reaction.
Epigenetic
Refers to factors affecting the development or function of an organism other than the primary sequence of the target genes.
See also Imprinting.
Episome
A plasmid able to integrate into bacterial DNA.
Epistasis
Masking of a phenotypic trait through the action of a mutant allele. For example, albinism (absence of pigment) is epistatic to coat color genes that determine black vs. brown fur in animals.
EST
Expressed Sequence Tag. A partial sequence of a randomly chosen cDNA, obtained from the results of a single DNA sequencing reaction. ESTs are used both to identify transcribed regions in genomic sequence and to characterize patterns of gene expression in the tissue that was the source of the cDNA.
Ethidium Bromide
A fluorescent dye that intercalates between base pairs in double-stranded nucleic acids or between bases in single-stranded nucleic acids. Ethidium bromide is commonly used to visualize DNA on agarose gels.
Etiology
  • The cause of a disease.
  • The genes identified as involved in causing a disease.
Euchromatin
The part of the genome characterized by relatively high gene density and relative absence of highly repetitive sequences.
See also Heterochromatin.
Eukaryote
A cell or organism with membrane-bound, structurally discrete nucleus and other well-developed subcellular compartments.
See also prokaryote.
Euploid
Having a chromosome number that is an integral multiple of the haploid number without segmental duplications or deletions.
Evidence Code
Unique identifiers that describe the types of evidence that support and justify the inclusion of information within a database. In PGDBs, evidence codes typically justify the existence of biological entities such as genes and pathways. Evidence codes are denoted by visual icons in the upper-right corner of pages such as pathway and enzyme pages. For example, a flask icon denotes experimental evidence [example]. Clicking on evidence icons will produce a more detailed explanation of the evidence type, and often a citation to the source of the evidence.
Evolution
Change of the genes of a population over time, resulting in new species.
Evolutionary Conservation
The presence of similar genes, portions of genes, or chromosome segments in different species, reflecting both the common origin of species and an important functional property of the conserved element.
Exon
Part of a gene whose sequence is present in a mature mRNA after splicing.
See also Intron.
Expressivity
The relative constancy of the phenotype of individuals of a given genotype. Mutations said to have variable expressivity show a relatively large amount of phenotypic variation among individuals having the same genotype.
See also Penetrance.
FBA Model
An FBA (Flux Balance Analysis) model predicts the steady-state flux rates of metabolic reactions given a set of nutrients, secretions, and biomass metabolites (the end products of biosynthesis). The Pathway Tools MetaFlux module provides FBA model development and solving capabilities through the locally installed version of Pathway Tools on the Linux and Mac platforms.
FFAQP : Free Form Advanced Query Page
FFAQP is a form that allows a user to enter the text form of a bioVelo query and submit that query for execution. The FFAQP allows users to enter more advanced queries than does the Structured Advanced Query Page because the full BioVelo query language is accessible from the Free Form page.
FASTA format
A data format for nucleic acid or protein sequences.
Field
In a relational database, an item of information, such as a chromosome number, or the centimorgan length on a genetic map. Some fields are numeric, while others are textual; some are long, while others are short. In addition, every field has a name, called the field name. In database management systems, a field can be required, optional, or calculated. A required field is one in which you must enter data, while an optional field is one you may leave blank. A calculated field is one whose value is derived from some formula involving other fields. You do not enter data into a calculated field; the system automatically determines the correct value. A collection of fields is called a record.
See also parameter.
Finished sequence
Sequence of genomic DNA in which: a) bases are identified to an accuracy of no more than one error in 10,000 bases, b) there is no ambiguity about the order or orientation of any segment, and c) there are few if any gaps.
See also Draft Genome Sequence.
FISH
Fluorescent in situ hybridization. A method for determining the cytogenetic location of a cloned segment of DNA. The DNA is labeled with a fluorescent dye and hybridized to a cytological preparation of chromosomes that has been denatured to allow nucleic acid hybridization between chromosomal DNA and the probe. The site of hybridization is determined by fluorescent microscopy. See the Figure at NHGRI.
See also In situ Hybridization.
Floxed
Refers to a DNA construct in which a gene or gene segment is flanked by loxP sites in the same orientation; Cre recombinase excises the segment between the loxP sites.
Fluorescence
Emission of secondary light generated by excitation by ultraviolet light, a beta particle or a gamma ray.
Fluorography
The detection of radiation or of a fluorescent compound by secondary light that was generated by the excitation of a "fluor" or a screen by light, a beta particle or a gamma ray.
Frameshift
A type of mutation in which there is an insertion or deletion that changes the reading frame.
Free-Text Format
A data format for nucleic acid or protein sequences.
FTP
File Transfer Protocol. A method for transferring files to and from remote computer systems.
Gain-of-function Mutation
A type of mutation in which the altered gene product possesses a new molecular function or a new pattern of gene expression. Gain-of-function mutations are almost always Dominant or Semidominant.
See also:
Gamete
One of the differentiated cells that is a product of meiosis. In animals, sperm or egg cells.
GCG Format
A data format for nucleic acid or protein sequences.
GenBank
The database of nucleic acid sequences at NCBI.
Gene
The basic unit of heredity; a portion of DNA that (usually) codes for a protein product.
See also Central Dogma.
The term "gene" may be used to refer to any of the following:
  1. A locus in the cytoplasmic or nuclear genome characterized by an altered phenotype or by an effect on an inserted reporter gene, such as a gene trap or enhancer trap.
  2. A locus in the cytoplasmic or nuclear genome that is necessary and sufficient to express the complete complement of functional products derived from a unit of transcription.
  3. A locus in the cytoplasmic or nuclear genome identified by hybridization to a nucleic acid segment derived from another species, where the segment used as probe represents some portion of a functional unit of transcription in the cytoplasmic or nuclear genome of the other species.
  4. An exon-encoding segment of the germ-line nuclear genome located within a region that undergoes somatic rearrangement.
  5. A locus in the cytoplasmic or nuclear genome that is within an intron of (but not, itself, an exon of) a unit of transcription, which gives rise to a functional product upon transcript processing of the host unit.
Gene Complex
A number of apparently functionally or evolutionarily related loci that are genetically closely linked. Alternative states of complexes are referred to as haplotypes rather than alleles.
Gene Conversion
A type of nonreciprocal recombination event in which a recipient strand of DNA receives information from another strand having an allelic difference. The recipient strand has its original allele "converted" to the new allele as a consequence of the event.
Gene Expression
Transcriptional activity of a gene resulting in one or more RNA products and, usually, following translation, one or more protein products.
Gene/reaction knockout experiments
This mode of MetaFlux predicts which genes (or reactions) are essential and which genes (or reactions) are not essential. It can also predict which biochemical reactions are essential. Multiple simultaneous knockouts of reactions and genes (i.e., single, double, and so on) are provided.
Gene Family
A group of paralogous genes.
Gene Model
A representation of an mRNA transcript of a gene that contains information about features of the transcript such as exon- intron boundaries, splice sites, UTRs, etc. Due to alternative splicing of mRNA transcripts, there may be more than one gene model for any given gene.
See also:
Gene Name
A "gene name" is a word or phrase that uniquely identifies a gene. The gene name has an abbreviation that is the gene symbol.
See also:
Gene Ontology (GO)
A set of controlled vocabularies used to describe biological features within a specified domain of biological knowledge. See the GO Consortium site for further information.
Gene Product
  1. A protein molecule that is the product of the expression of a gene, through which the gene influences development or metabolism.
  2. An RNA molecule that is the product of the expression of a gene, specially those cases in which the RNA molecule is not translated (see tRNA, rRNA).
Gene Symbol
A "gene symbol" is a unique abbreviation for the gene name.
See also:
Genetic Code
The relationship of the sixty-four nucleic acid codons to the twenty primary amino acids. See the Figure for the standard genetic code.
See also Central Dogma.
Genetic Map
A map showing the position of genes or markers on a chromosome.
See also:
Gene Trap
A type of DNA construct containing a reporter gene sequence downstream of a splice acceptor site that is capable of integrating into random chromosomal locations. Integration of the gene trap into an intron allows the expression of a new mRNA containing one or more upstream exons followed by the reporter gene. The reporter gene is therefore expressed in the same cells and developmental stages as the gene into which the gene trap has inserted.
See also Enhancer Trap.
Genome
The total genetic information of a cell or organelle. In eukaryotes, "genome" usually refers to nuclear DNA rather than to mitochondrial or chloroplast DNA.
Genomics
The comprehensive study of whole sets of genes and their interactions rather than single genes or proteins.
Genotype
  1. A description of the genetic information carried by an organism. In the simplest case, genotype may refer to the information carried at a single locus, as in A/A, A/a, or a/a.
  2. The genetic constitution of an organism, as distinguished from its physical appearance (its phenotype).
Genome Browser
A genome browser is a graphical interface used to examine the layout of genes and other features within a replicon (chromosome or plasmid). The comparative genome browser can be used to examine several replicons (chromosomes or plasmids) simultaneously side by side. This allows easy visual comparison of related organisms to observe similarities and differences in their gene arrangements.
Genome Overview
The Genome Overview shows in one screen all the genes in an organism's genome, as well as additional information about their transcription units and products.
Genome Poster
A poster-size depiction of the genome map (replicons) of an organism, generated from a PGDB by the Pathway Tools genome browser.
Germ Line
Cells of an animal that give rise to gametes.
Groups
The Pathway Tools Groups feature can be used to create collections of related objects that are interesting in some way, in order to process, analyze, display or export them as a unit.
Guanine (G)
A purine base that is a component of nucleotides and thus a normal component of DNA and RNA. See the Figure at NHGRI.
Haploid
Having the chromosome number normally found in a gamete.
See also Diploid.
Haploinsufficient
A description applied to a gene that produces a mutant phenotype when present in a diploid individual heterozygous for an amorphic allele.
Haplotype
One of the alternative forms of the genotype of a gene complex. This term is applied to gene complexes rather than the term allele, which refers to one of the forms of a single gene.
Hemizygous
The state of a locus in a diploid organism, where only one copy of the locus is present. Examples are sex-linked genes in normal mammalian males, insertions such as transgenic insertions, and autosomal alleles in combination with deletions that remove entire gene regions.
Heterochromatin
  1. The part of the genome characterized by relatively low gene density and the presence of highly repetitive sequences. Heterochromatin is more highly condensed than euchromatin.
  2. The X chromosome that is highly condensed in a mammalian cell that has undergone X inactivation. The inactive X chromosome resembles heterochromatin as defined above with respect to their state of condensation and genetic inactivity, although there is no change in the DNA sequence as a consequence of inactivation.

See also Euchromatin.
Heterogametic
Producing two types of euploid gametes with respect to chromosomal content. This term is applied to one of the sexes in species with chromosomal sex determination; in mammals, males are heterogametic.
See also:
Heteropolymer
A polymer composed of different subunits. Some multimeric proteins are normally heteropolymers. Heteropolymers can also be made experimentally, using subunits derived from different species, as a test of homology. Formation of a functional multimeric protein product using subunits from different species is a demonstration of homology.
Heterozygosity
The state of being heterozygous.
Heterozygote
An individual that is heterozygous.
Heterozygous
The state of a diploid locus in which different alleles are present at the two copies of that locus (usually one is normal and the other is abnormal).
Hierarchical
A description of a structure in which things are organized into a hierarchy.
Hierarchy
An organization with few things, or one thing, at the top and with several things below each other thing. An inverted tree structure. An example in computing is a directory hierarchy where each directory may contain files or other directories. It may refer to terms in a controlled vocabulary such as ones containing Gene Ontology (GO) terms.
Hole Filler
The Pathway Tools Pathway Hole Filler provides a computational method for combining evidence from homology data, operon-based data, and pathway context to identify missing enzymes in a Pathway/Genome Database (see also: Pathway Hole).
Homogametic
Producing a single type of euploid gametes with respect to chromosomal content. This term is applied to one of the sexes in species with chromosomal sex determination; in mammals, females are homogametic.
See also:
Homolog
  1. One of a pair of chromosomes that segregate from one another during the first meiotic division.
  2. A gene related to a second gene by descent from a common ancestral DNA sequence. The term, homolog, may apply to the relationship between genes separated by the event of speciation (see ortholog) or to the relationship betwen genes separated by the event of genetic duplication (see paralog).
  3. A morphological structure in one species related to that in a second species by descent from a common ancestral structure.
Homologous recombination
  1. Reciprocal recombination between DNA sequences that have a high degree of similarity.
  2. Reciprocal recombination between DNA sequences that have a high degree of similarity and that are located at corresponding positions on homologous chromosomes.
Homology
The relationship of any two characters that have descended from a common ancestor. This term can apply to a morphological structure, a chromosome or an individual gene or DNA segment. See the Figure at NCBI.
See also:
Homozygosity
The state of being homozygous.
Homozygote
An individual that is homozygous.
Homozygous
The state of a diploid locus in which identical alleles are present at both copies of that locus.
Horseradish Peroxidase
An enzyme for which a chromogenic substrate exists, commonly used as a label for antibodies.
HTML
Hypertext Markup Language. An authoring language for creating and sharing electronic documents over the Internet. You can view the HTML source code for a web page by selecting the Source view from one of your browser's menus.
Hybrid
  1. The offspring of two sexually-reproducing homozygous individuals of different genotypes.
  2. As a mapping data type, a somatic cell hybrid experiment.
Hybridization
With respect to nucleic acids, "hybridization" refers to the formation of double-stranded DNA, RNA, or DNA/RNA hybrids by complementary base pairing.
Hydrophilic
Literally, "water-loving"; polar or charged compounds that are soluble in water.
Hydrophobic
Literally, "water-fearing"; nonpolar compounds that are immiscible with water. The side chains of some amino acids are nonpolar, and hence protein sequences rich in these amino acids tend to locate to the interior of the protein in its native state, away from the solvent.
Hypermorphic Mutation
A type of mutation in which the altered gene product possesses an increased level of activity, or in which the wild-type gene product is expressed at a increased level.
See also:
Hypertext
Text displayed electronically with embedded links to other text or to images, sounds, movies or other multimedia content. This document is an example of hypertext.
Hypomorphic Mutation
A type of mutation in which the altered gene product possesses a reduced level of activity, or in which the wild-type gene product is expressed at a reduced level.
See also:
Identity
In comparison of nucleic acid or protein sequences, the extent to which two sequences have the same nucleotide or amino acid at equivalent positions, usually expressed as a percentage.
See also Similarity.
Idiogram
An idealized drawing. See the idiogram of the mouse karyotype at the Department of Pathology at the University of Washington.
IMAGE Consortium
Integrated Molecular Analysis of Genome Expression Consortium. A collection of a large number of partially sequenced cDNAs. See the homepage of the IMAGE Consortium for further information.
Immunofluorescence
The detection of an antigen in cytological preparations by using a fluorescent-labeled antibody.
Immunohistochemistry
A method of detecting the presence of specific proteins in cells or tissues. Fixed cells or tissue on a microscope slide, made permeable if necessary with a detergent, are reacted with a primary antibody to the specific protein to be assayed. The preparation is then treated with a secondary antibody that has been coupled to an enzyme and which is directed against the primary antibody (e.g., goat anti-rabbit antibody). The preparation is then treated with a chromogenic substrate. Microscopic examination reveals the presence of staining, and hence of the specific protein to be detected.
Immunological Cross-reaction
The binding of an antibody to a protein that is different from the protein against which the antibody was raised. This result demonstrates sequence or structural similarity between the two proteins and can be evidence of homology.
Imprinting
An epigenetic modification of genes that identifies a given gene as having been inherited from the maternal or paternal parent. In mammals, some genes are expressed primarily from the maternally-inherited or paternally-inherited alleles as a consequence of imprinting.
Inbred Strain
A strain that is essentially homozygous at all loci. In mice, a strain produced from brother-sister matings for at least 20 sequential generations. C57BL/6J is a widely-used inbred strain of mouse.
Incross
A cross between two identically homozygous individuals (A/A X A/A).
See also:
Informatics
The study of the application of computer and statistical techniques to the management of information. In genome projects, Informatics includes the development of methods to search databases quickly, to analyze DNA sequence information, and to predict protein sequence and structure from DNA sequence data.
Inheritance Mode
The manner in which a particular genetic trait is expressed when passed from one generation to another (for example, dominant, recessive, semidominant, etc.).
Inhibitor
A chemical compound that has the effect of blocking or slowing an enzymatic reaction.
Insertion
A type of mutation in which one or more nucleotides is inserted into a DNA sequence. Small insertions within a gene can alter the reading frame, and thus the amino acid sequence of the encoded protein.
In silico
Computationally, as opposed to in vitro or in vivo.
In situ Hybridization
A method of detecting the presence of specific nucleic acid sequences within a cytological preparation. A DNA or RNA probe is labeled radioactively or chemically and hybridized to a cytological preparation to detect RNA or to a denatured cytological preparation to detect DNA. The hybridization is detected by autoradiography (for radioactive probes) or by chromogenic reactions or fluorescence (for chemically-labeled probes).
See also FISH.
In situ Reporter (Knock in)
An assay type that uses mice containing a targeted mutation in which a reporter gene has replaced an endogenous gene. The two most common reporter genes are lacZ and green fluorescent protein.
See also Knock in.
Intercross
A cross between two identically hybrid individuals (A/a X A/a).
See also:
Intergenic
Between genes.
Intergenic Distance
Intergenic distance is the number of base pairs between genes.
Interim
A term appended to a gene symbol that is under review.
InterPro domain
One of a collection of amino acid sequences of identifiable features in known proteins that can be compared to unknown protein sequences. See InterPro at EMBL/EBI.
Intron
Part of a gene whose sequence is transcribed but not present in a mature mRNA after splicing.
See also Exon.
Inversion
A type of mutation in which a length of DNA is broken in two positions and repaired in such a way that the medial segment is now present in reverse order. Inversions range in size from those large enough to be visible cytogenetically to those involving only a few base pairs.
In vitro
Literally, "in glass", meaning a reaction, process or experiment in a metaphorical test tube rather than in a living organism.
See also:
In vivo
Literally, "in life", meaning a reaction, process or experiment in a living organism rather than in a metaphorical test tube.
See also:
Isogenic
Characterized by essentially identical genes. Identical twins are isogenic.
Karyotype
A description of the condensed chromosomes of a eukaryote as they are seen at metaphase. Additional details are revealed by a variety of staining techniques that produce banded chromosomes. See the idiogram of the mouse karyotype at the Department of Pathology at the University of Washington.
kb
Kilobase. Unit of DNA or RNA sequence equal to 1000 nucleotides.
Kinetochore
A structure formed adjacent to the centromere of a condensed chromosome that allows the chromosome to attach to microtubules of the meiotic or mitotic spindle.
Knock in
A casual term for a type of targeted mutation in which an alteration in gene function other than a loss-of-function allele is produced.
See also Knock out.
Knock out
A casual term for a type of targeted mutation in which an amorphic (loss-of-function) allele is produced.
See also Knock in.
Library
In molecular biology, a "library" is a complex mixture of recombinant DNA molecules in a suitable cloning vector representing either the entire genome of an organism (a genomic library) or the messenger RNA population of a whole organism, cell type, or tissue type (a cDNA library).
Ligand
A ligand is the thing that a protein binds.
Ligate
In molecular biology, to join two separate DNA or RNA segments to form a single DNA or RNA molecule enzymatically.
Linkage
The property displayed by two genes that do not segregate independently of each other. Genes that are linked are on the same chromosome.
Linkage Analysis
The construction of a linkage map through the analysis of meiotic recombination frequencies between pairs of genes.
Linkage Map
A type of genetic map showing relative gene positions based on meiotic recombination frequencies. The unit of measurement is the centimorgan.
See also:
Locus
Literally, "place". The location of a gene or set of genes on a chromosome.
LOD score
A statistical estimate of whether two loci are likely to lie near each other on a chromosome and are therefore likely to be inherited together. Lod stands for "log of the odds ratio." In this case, the odds ratio is the likelihood that two markers are linked divided by the likelihood that they are not linked. A LOD score of three or more is generally taken to indicate that the two loci are close.
Loss of Heterozygosity
A genetic event that can occur in the dividing cells of a diploid organism heterozygous for one or more markers, in which a daughter cell becomes homozygous or hemizygous for one or more alleles through mitotic recombination, deletion, or gene conversion. "Loss of heterozygosity (LOH)" events are often important steps in tumor progression.
loxP Sequence
A 34 base pair DNA sequence recognized by the site-specific recombination enzyme Cre.
Marker
  1. Any biological feature that can be positioned with respect to other features on a chromosome, by genetic, physical or other mapping methods. For example, a gene, anonymous DNA segment, mutation, or phenotype.
  2. A feature that distinguishes a particular biological state. For example, an expression profile of natural or engineered genes, or a characteristic morphology.
Master Regulator
A gene involved in controlling the expression of a large number of genes.
Megabase
Unit of DNA or RNA sequence equal to one million nucleotides.
Meiosis
A pair of nuclear divisions forming gametes wherein the number of chromosomes is reduced from the diploid to the haploid number; resulting cells normally contain one member of each pair of homologous chromosomes.
Membrane
  1. A phospholipid bilayer that forms a hydrophobic barrier around and within cells.
  2. A sheet of nylon, nitrocellulose, or similar material used to create a replica of a gel for Southern blots, Northern blots, or Western blots.
Mendelian
  1. That type of inheritance in which a specific trait is affected by a set of alleles of a single gene.
  2. That type of inheritance in which genetic information is transmitted by one or more nuclear genes, as opposed to cytoplasmic or epigenetic mechanisms.
Metabolic Cluster
A metabolic cluster is a Pathway Tools term for a set of biochemical reactions that are biologically related, but are largely unconnected, and therefore do not constitute a pathway in the traditional sense of the word.
Metabolic Poster
A poster-size depiction of the Cellular Overview diagram generated from a PGDB by Pathway Tools.
Metabolite Tracing
The Metabolite Tracing facility of Pathway Tools permits users to graphically trace the path of a metabolite through the metabolic network.
MetaCyc
A Pathway/Genome Database describing experimentally elucidated metabolic pathways and enzymes. MetaCyc is both an online reference source on metabolic pathways, and is a reference database for computational prediction of metabolic pathways. MetaCyc is available at URL MetaCyc.org. MetaCyc is a member of the BioCyc Database Collection.
Metadata
Data about data. In data processing, metadata is definitional data providing information about or documentation of other data managed within an application or environment, for example, data about
  • data elements or attributes (name, size, data type, etc.),
  • records or data structures (length, fields, columns, etc.) and
  • data (where located, how associated, what ownership, and so on).
Metadata may include descriptive information about the context, quality and condition, or characteristics of the data.
MetaFlux
The FBA Module of the Pathway Tools is called MetaFlux. See the Pathway Tools Overview for more information.
Microarray
An array of hundreds or thousands of spots containing specific DNA sequences for the analysis of gene expression by hybridization. Microarrays are used to detect changes in gene expression by comparing radioactively- or chemically-labeled cDNA prepared from the total mRNA of an experimental sample to that of a control sample. The relative intensity of the signal corresponding to each spot in the microarray reveals whether the expression of a particular gene is increased, decreased, or unchanged in the experimental mRNA sample compared to the control mRNA sample.
MicroRNA
MicroRNAs (miRNAs) are a group of noncoding RNA molecules, generally 21 to 24 nucleotides in length, which are usually cleaved from a larger hairpin-containing RNA (itself often processed from some portion of mRNA). miRNAs are conserved through evolution, and their abundance and expression patterns are suggestive of diverse regulatory roles.
Microtubule
A cytoskeletal element of eukaryotic cells that is a long, generally straight, hollow tube with an external diameter of 24 nm, consisting of polymerized monomers of tubulin. Microtubules make up the bulk of the spindle.
Mitochondria
The organelles that generate energy in eukaryotic cells. Mitochondria have their own genome encoding a subset of the proteins found in mitochondria; the mitochondrial genome uses an alternate genetic code.
Mitochondrial gene
A gene contained within the mitochondrial genome of a eukaryote, transmitted independently of the nuclear genome. The mitochondrial genome is transmitted maternally (from the female parent).
Mitosis
The division of the replicated chromosomes of a eukaryotic cell into two daughter nuclei that are genetically identical to that of the original cell. See the Figure at NHGRI.
Mobile Genetic Element
A DNA segment carried within the chromosomes that is capable of moving to new sites in the genome other than by mutation.
See also Retrotransposon.
Model Development Mode (MetaFlux)
This mode of MetaFlux generates an accurate and feasible FBA model for a PGDB (i.e., an organism).
Model Organism Database
A database that describes the genome of an organism, plus other information. A Pathway/Genome Database is a type of model-organism database. The organism may or may not be a model for studying some biological process --- the term "organism-specific database" could be used equally well, but "model-organism database" (MOD) has been used historically in bioinformatics. MODs provide a central resource where new computational and experimental findings about a genome can be integrated and reviewed by experts for that organism. MODs serve as a distributed collaboration framework that allows a set of experts to collaboratively develop a complex DB that serves as a platform for disseminating the genome and its analyses to the scientific community. MODs are indispensable resources in the day-to-day work of experimentalists for a given organism, who use them as reference sources for genome information, gene annotations, pathways, and regulatory information.
Molecular Function
Refers to the tasks or activities characteristic of particular gene products. For example, transcription factor refers to one of a number of proteins performing similar tasks. In the GO Project vocabularies, Molecular Function is a primary class of terms. See the GO Consortium site for further information.
Molecular Mutation
A description of the type of molecular event giving rise to a specific mutation, for example, deletion, inversion, point mutation, and so on.
Monoclonal Antibody
An antibody produced by cultured cells that have their origin in a single antibody-producing cell and which is therefore of a single molecular type, in contrast to the polyclonal antibodies normally found in the serum of an immunized animal.
Monosomy
The condition of having a single chromosome of a particular type; lacking a homologous chromosome. Normal male mice are monosomic for the X chromosome.
See also Trisomy.
Mosaic
An individual consisting of cells of two or more genotypes. One example is that of a normal female mammal heterozygous for different alleles of X-chromosome genes; because of the process of X-inactivation, such females consist of two cell types, each with a different X chromosome inactivated. This is an unusual example because there is no actual difference in genotype between the two cell types, but rather there is an epigenetic difference.
mRNA
Messenger RNA. An RNA molecule that is the product of transcription of a gene. In eukaryotes, that molecule often has to be spliced and polyadenylated before it can be translated into a protein product. See the Figure at NHGRI.
See also Central Dogma.
Multi-Genome Browser
The Multi-Genome Browser displays chromosomal regions for multiple organisms centered on corresponding genes.
Mutagen
An agent that causes mutations.
Mutant
  1. A term applied to a gene or phenotype altered by mutation.
  2. An individual carrying a mutation.
Mutant ES Cell Line
A specific sub-line of embryonic stem (ES) cells containing an introduced mutation.
Neomorphic Mutation
A type of mutation in which the altered gene product possesses a novel molecular function or a novel pattern of gene expression. Neomorphic mutations are usually dominant or semidominant.
See also:
Noncoding RNA
An RNA molecule that functions structurally or catalytically (see ribozyme) without being translated. Noncoding RNAs lack conserved open reading frames. One example is 23S ribosomal RNA.
Non-Mendelian
  1. That type of inheritance in which a specific trait is affected by a set of alleles of a multiple genes. Synonym: Polygenic
  2. That type of inheritance in which genetic information is transmitted other than by nuclear genes. See Epigenetic, Mitochondria.
Northern Blot
An assay that detects specific RNA molecules using a DNA or RNA probe with sequence similarity. Samples are subjected to electrophoresis on a slab gel. A replica of the gel is then made on a membrane by capillary transfer. Specific RNA sequences are then detected on the membrane with a radioactively- or chemically-labeled probe.
See also:
Nucleic Acid
DNA or RNA. Each of these compounds consists of a backbone of sugar molecules ribose for RNA and deoxyribose for DNA linked by single phosphate groups. Attached to the sugars of the backbone are any of four nitrogenous bases, A, T, C or G for DNA and A, U, C or G for RNA. See the Figure at NHGRI.
Nucleotide
A monomer unit of nucleic acid, consisting of a purine or pyrimidine base, a sugar molecule (ribose or deoxyribose), and phosphate group(s).
Nucleotide Repeat Expansion
A type of mutation in which a set of tandemly repeated sequences replicates inaccurately to increase the number of repeats. An example of this kind of mutation in humans is the FMR1 gene.
Nucleotide Substitution
A point mutation.
Nucleus
The organelle in a eukaryotic cell that contains the chromosomes. In most types of eukaryotic cells, the nucleus breaks down as chromosomes condense during cell division. See the Figure at NHGRI.
Null
In mathematics, a set with no members or of zero magnitude. If a field has a value of null, it means that the value is unknown. A null value is not the same as a value of zero. (To appreciate the difference, consider the terms "free" and "priceless." If something is free, it has a price of zero. If something is priceless, it has no known price. The difference between null and zero can be crucial; for example, when calculating the average value of a field among many records where one row contains a zero, the zero gets factored into the average. If the field has a null value, it does not get factored into the average.)
Numerical Aberration
A change in the number of chromosomes from the wild-type number in the absence of any chromosome rearrangement.
See also:
Oligonucleotide
A short length of nucleic acid.
Omics Viewer
The Pathway Tools omics viewer uses the Cellular, Regulatory and Genome Overviews to illustrate the results of high-throughput experiments in a global metabolic and genomic context by painting experimental data onto these diagrams.
OMIM
Online Mendelian Inheritance in Man. A database of human inherited diseases and genes.
Ontology
Ontologies are used to structure biological knowledge such that the knowledge can be manipulated computationally. One type of ontology is a controlled vocabulary, meaning a list of biological terms, each of which contains an English definition, and a unique identifier. Databases refer to that term by its unique identifier to avoid ambiguity, such as the ambiguity that occurs when the same word has multiple meanings. Another type of ontology is an "is-a" hierarchy in which terms in a controlled vocabulary are arranged in a generalization hierachy (or hierarchical classification) such that one term is a parent of another term if the first term denotes a more general concept than the second term. For example, the MetaCyc database contains a hierarchical classification of metabolic pathways. Hierarchical classification systems allow users to retrieve related sets of objects within the database, and to drill down from more general to more specific classes of information. Database schemas and knowledge representation systems are also types of ontologies.
Open Reading Frame (ORF)
A length of nucleotide sequence that lacks termination codons in a given reading frame.
Operons
A unit of genetic material that is expressed in a coordinated manner by means of an operator, a promoter, and one or more structural genes that are transcribed together.
Organelle
One of a number of different kinds of membrane-bound substructures within a eukaryotic cell. Examples include the nucleus, mitochondria, and chloroplasts.
Ortholog
One of a set of homologous genes that have diverged from each other as a consequence of speciation. For example, the alpha globin genes of mouse and chick are orthologs. See the Figure at NCBI.
See also:
Orthology
The relationship of any two homologous characters whose common ancestor lies in the most recent common ancestor of the taxa being considered.
See also:
Outcross
A type of genetic cross in which an organism is crossed to a strain from which it was not recently derived.
See also:
P1
A bacteriophage with a genome size of over 100 kb that has been used as a cloning vector.
PAC
P1 Artificial Chromosome. A type of cloning vector derived from bacteriophage P1 that allows foreign DNA segments to be cloned in bacteria. The capacity of a PAC is up to 100 kb of foreign DNA.
PathoLogic
The inference component of the Pathway Tools software. PathoLogic contains four predictors: A predictor of metabolic pathways; a predictor of missing enzymes in metabolic pathways (the pathway hole filler); an operon predictor; and a program that predicts transport reactions from transporter functional descriptions. See the Pathway Tools Overview for more information.
Pathway
An interconnected set of biochemical reactions, where reactions are connected by sharing common reactants and products. In metabolic pathways, reactants and products are typically low-molecular-weight chemical compounds. In signaling pathways, reactants and products are typically proteins.
Pathway/Genome Database
A Pathway/Genome Database (PGDB) is a database managed by SRI's Pathway Tools software that describes an information space ranging from genomes to pathways. A PGDB such as EcoCyc describes the genome of an organism, the product of each gene, the biochemical reaction(s) catalyzed by each gene product, the substrates of each reaction, and the organization of reactions into pathways. The schema of a PGDB can also describe the regulatory network of an organism.
Pathway Tools Overviews
A genome-scale depiction of information within a PGDB. There are three different Overviews: the Cellular Overview depicts the metabolic network, the Regulatory Overview depicts the regulatory network, and the Genome Overview depicts the full genome.
Pathway Tools Posters
Pathway Tools can generate postscript and/or PDF files of a poster-size depiction of a genome map and of a metabolic map from a PGDB.
Paralog
One of a set of homologous genes that have diverged from each other as a consequence of genetic duplication. For example, the mouse alpha globin and beta globin genes are paralogs. The relationship between mouse alpha globin and chick beta globin is also considered paralogous. See the Figure at NCBI.
See also:
Paralogy
The relationship of any two homologous characters that arose by a genetic duplication.
See also:
Parameter
An item of information such as a name, a number, or a selected option passed to a program by a user or another program. Parameters affect the operation of the program receiving them. Parameters are values that you select or enter in the query form fields.
Pathway Evidence Report
Pathologic can generate a “pathway evidence report” Web page that lists all pathways it has predicted in an organism and the evidence supporting each predicted pathway. This report provides a convenient way for a scientist to review the evidence for each pathway.
Pathway Holes
A pathway hole is a pathway reaction thought to occur in an organism for which no corresponding enzyme has been identified in the genome.
Pathway Tools
The SRI software system used to construct, update, visualize, query, and analyze Pathway/Genome Databases (PGDBs). Pathway Tools powers the BioCyc website and other similar websites. It can also be installed locally as a desktop application. Pathway Tools has four components: (1) The Pathway/Genome Navigator supports querying, visualization, and analysis of PGDBs. (2) The PathoLogic program supports automated creation of a PGDB and performs several computational inferences including prediction of the metabolic pathway complement and operons of an organism. (3) MetaFlux is used to develop steady-state metabolic flux models from PGDBs using flux-balance analysis. (4) The Pathway/Genome Editors support interactive updating and refinement of PGDBs. Pathway Tools was developed by the group of Dr. Peter D. Karp at SRI International.
Parent
In BioCyc, this term refers to terms in a hierarchical controlled vocabulary such as those containing Gene Ontology (GO) terms. A "parent" of a term is one any number of levels above it in the hierarchy from which it is descended. For example, the GO term enzyme [GO:0003824] is a parent to the GO term alcohol dehydrogenase [GO:0004022].
See also:
PCR
Polymerase Chain Reaction. A method of amplifying specific DNA segments based on hybridization to a primer pair. A DNA sample is denatured by heating in the presence of a vast molar excess of short single-stranded DNA primers (around 20 nucleotides) whose sequence is chosen based on the target sequence. The reaction mixture also contains a thermostable DNA polymerase, dNTPs, and buffer. The primer sequences are selected so that they:
  1. are derived from opposite strands of the target sequence,
  2. have their 3' ends facing each other, and
  3. are separated by a length of DNA that can be reliably synthesized in vitro.
The sample is then cooled to a temperature that allows primer annealing and in vitro replication. The sample is subjected to multiple cycles of denaturation and cooling to allow multiple rounds of replication. The quantity of the target sequence doubles during each cycle, causing the target sequence to be amplified, while other DNA sequences in the sample remain unamplified. See the Figure at Access Excellence.
Penetrance
The fraction of individuals of a given genotype that show a particular phenotype, usually expressed as a percentage.
See also Expressivity.
PGDB Registry
The PGDB registry is an Internet-based mechanism for sharing PGDBs among Pathway Tools users.
Phage
  1. A bacteriophage, a virus capable of infecting bacteria.
  2. A type of cloning vector derived from a bacteriophage, usually capable of carrying an amount of foreign DNA that is at the upper range of that carried by a plasmid.
Phagemid
A type of cloning vector derived from a phage and a plasmid. Phagemids are capable of carrying an amount of foreign DNA comparable to a plasmid, but have some special feature such as the ability to produce single-stranded DNA.
Phenocopy
The condition of an individual resembling that of a phenotype produced by a particular mutation by some experimental treatment other than the presence of that mutation, e.g., drug treatment.
Phenotype
A description of the observable state of an individual with respect to some inherited characteristic. Often, individuals with different genotypes display the same phenotype. See dominant and recessive.
Phosphorimaging
The detection of radioactivity using "phosphor" compounds that emit visible light when exposed to radiation. Phosphorimaging instruments produce images of, for example, Southern blots and Northern blots, that are comparable to those produced by autoradiography, with superior quantitation.
Phycoerythrin
A fluorescent dye that can be coupled to antibodies for the detection of proteins on Western blots using fluorography.
Physical Map
A map of DNA showing distances between and within genes or specified markers measured in base pairs of DNA. It is based on the direct measurement of DNA.
See also:
Plasmid
A type of cloning vector derived from autonomously-replicating extrachromosomal circular DNAs in bacteria. The amount of foreign DNA that can be carried in a plasmid is small, ranging up to about 20 kb.
Pleiotropy
The production of a phenotype affecting multiple traits by a single mutation.
Point Mutation
A type of mutation in which a single nucleotide is changed to one of the other three possible nucleotides.
See also:
Polyadenylation
The process by which a series of adenosine (A) ribonucleotides is added to the 3' end of a spliced RNA to make a mature mRNA. This addition to the RNA is sometimes referred to as a poly-A tail, and commonly contains several hundred bases.
Polygenic
A trait determined by multiple genes.
Polymorphism
An instance of genotypic variation within a population.
Primary Metabolism
Metabolism is the term used to describe all of the chemical reactions and interactions that take place in a biological system. Primary metabolism encompasses reactions involving those compounds which are formed as a part of the normal anabolic and catabolic processes which result in assimilation, respiration, transport, and differentiation. These processes take place in most, if not all, cells of the organism. Common examples of primary compounds are sugars, amino acids, nucleotides etc. Primary metabolism is simply defined as the metabolism of primary compounds.
Primer
A single-stranded nucleic acid that can "prime" replication of a template. More specifically, a single-stranded nucleic acid capable of hybridizing to a template single-stranded nucleic acid in such a way as to leave part of the template to the 3' end of the primer single-stranded. DNA polymerase can then synthesize a new strand starting from the 3' end of the primer and adding nucleotides to the growing strand by base complementarity to the template.
See also PCR.
Probe
In molecular biology, a nucleic acid that has been labeled either radioactively or chemically that allows the detection of nucleic acids with sequence similarity in a sample by hybridization. Probes are used to detect DNA on membranes in Southern blots, to detect RNA on membranes in Northern blots, and either DNA or RNA in cytological preparations for in situ hybridization.
Prokaryote
Cell or organism lacking a membrane-bound, structurally discrete nucleus and other subcellular compartments. Bacteria are prokaryotes.
See also eukaryote.
Promoter
One of the necessary regulatory elements of a gene. The promoter is the site on DNA to which RNA polymerase binds and initiates transcription.
See also Enhancer.
Protein
A polymer of amino acids. See the Figure at NHGRI.
Protein Domain
A region of a protein responsible for a particular function, as recognized experimentally and by the occurrence of similar segments in other proteins sharing that function, e.g., a DNA binding domain.
Protein Gene
A gene whose product is a protein.
Protein Histochemistry
  1. A method of detecting a particular enzyme in a cell or tissue sample. A sample of cells or tissue is fixed, then treated with a chromogenic substrate for the enzyme to be detected. Microscopic examination reveals the presence of staining, and hence of the specific protein to be detected.
  2. Immunohistochemistry.
Proteome
The complete collection of all proteins encoded by the genome of an organism.
Proteomics
Systematic analysis of protein expression of normal and diseased tissues that involves the separation, identification and characterization of all of the proteins in an organism.
Pseudoautosomal
The small region of homology shared between the X chromosome and the Y chromosome in mammals. All crossovers between the X and Y chromosomes occur in this region.
Pseudogene
A non-functional locus derived from a functional locus either by
  1. replicative transfer, such as transposition, retrotransposition or duplication or by
  2. mutation, where the non-functional locus is not considered an allele of an existing functional locus.
Purine
One of the bases of nucleic acids, either adenine (A) or guanine (G). See the Figure at NHGRI.
Pyrimidine
One of the bases of nucleic acids, cytosine (C), thymine (T) or uracil (U). See the Figure at NHGRI.
Quantitative Trait Locus (QTL)
  1. A heritable genetic region that affects a measurable characteristic of the animal (e.g., body weight or blood pressure).
  2. The type of marker described by statistical association to quantitative variation in a particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci.
Query
A request for information submitted to a computerized database.
See also:
Query Form
A Query Form is a web page allowing users to retrieve information from a database.
See also:
Query Sequence
A DNA or protein sequence submitted to a computerized database for comparison, e.g., a BLAST search.
See also:
Radiation
  1. Electromagnetic energy: gamma rays, X rays, ultraviolet light, visible light, infrared light, microwaves and radio waves. In mouse genetics, this term generally refers to gamma rays and X rays.
  2. Subatomic particles emitted by the decay of unstable isotopes: electrons (beta particles) and helium nuclei (alpha particles). Common unstable isotopes in molecular biology are tritium (3H),which emits low-energy beta particles, 35S, which emits beta particles of moderate energy, and 32P, which emits high-energy beta particles.
  3. Subatomic particles from a particle accelerator, such as protons, neutrons, and electrons.
Radiation Hybrid Mapping
A type of genetic mapping providing resolution between relatively low-resolution linkage analysis and high-resolution physical mapping by the assembly of contiguous cloned DNA segments. The method consists of fusing irradiated cultured cells of one species with cultured cells of a different species. A panel of hybrid cells is then tested for the occurrence of pairs of markers. The closer two markers are to each other, the more likely that both are present in an individual hybrid cell.
Radiation Induced Mutation
A mutation induced by irradiation, in mouse usually gamma-ray or X-ray.
RDBMS
Relational Database Management System. Software for managing a database accessed using Structured Query Language (SQL).
Reachability Analysis
Given a starting set of metabolites (called the nutrients), the Pathway Tools Reachability Analysis tool determines which reactions can fire, and which other metabolites are produced as a result of this qualitative simulation, in an automated and iterative manner.
Reading Frame
One of three ways of reading a single strand of nucleic acid sequence as codons.
Recessive
One of a series of terms applied to the phenotypic effect of a particular allele in reference to another allele (usually the standard wild-type allele) with respect to a given trait. An allele "a" is said to be recessive with respect to the allele "A" if the A/A homozygote and the A/a heterozygote are phenotypically identical and different from the a/a homozygote. An example is the nonagouti (a) allele of the mouse. A(+)/A(+) and (+)/a mice have identical agouti banding of individual hairs in the coat, while a/a mice have hairs of uniform color.
See also:
Recombination
Transfer of information from one DNA molecule to another. Recombination may be reciprocal, in which case the products are equivalent to breakage of the two DNA molecules and rejoining of the broken ends to form new molecules. Recombination may also be nonreciprocal, in which case the product is equivalent to transfer of information from the donor DNA molecule to the recipient DNA molecule, with no change in the donor DNA molecule. Reciprocal recombination events are also called crossovers.
Record
In computer science, a collection of fields.
Redox Half reactions
Redox half reactions are elementary reactions in which explicitly stated electrons are reducing an oxidized molecular species. These reactions do not stand alone, because electrons do not occur freely. Instead, a half reaction must be paired with another half reaction to form a complete, overall transformation.
RefSeq
The collection of integrated, non-redundant sequences including genomic DNA, transcript (RNA), and protein products at NCBI.
Regulatory Element
A DNA sequence that is required for a gene on the same DNA molecule to be transcribed, or to be transcribed in the proper cell type(s) and developmental stage(s).
See also:
Regulatory Gene
A gene whose function is to regulate the expression of a structural gene.
Regulatory Overview
The Regulatory Overview is a whole-organism depiction of the transcriptional regulatory network.
Relational Database
A type of database in which information is organized into tables.
Relational Database Management System (RDBMS)
Software for managing a database accessed using Structured Query Language (SQL).
Relative Data Values, Omics Viewer
The numerical values in the data file include positive and negative values.
Replication
The process of synthesizing a copy of a DNA molecule from nucleotides using information contained within one strand of a template DNA molecule. The new strand of DNA is synthesized from the 5' end to the 3' end. See the Figure at NHGRI.
Reporter Gene
A gene whose product is easily detected and not ordinarily present in an organism or cell type under study that is expressed as part of a DNA construct introduced experimentally. Bacterial beta-galactosidase, whose activity can be detected using a staining reaction, is a commonly used reporter gene, as is green fluorescent protein.
See also:
Restriction Enzyme
A protein that recognizes specific, short nucleotide sequences and cuts DNA at those sites.
Restriction Fragment
A length of DNA whose ends are the result of cutting by a restriction enzyme.
Retrotransposon
A type of mobile genetic element that utilizes an RNA intermediate and reverse transcriptase to transpose.
Retrovirus
A virus whose primary genetic material is RNA instead of DNA. Replication of the genome of such a virus requires the RNA to be copied into DNA using reverse transcriptase. This group of viruses includes HIV (AIDS virus).
Reverse Transcriptase
An enzyme that is able to synthesize DNA from information in RNA. It requires an RNA template and a DNA or RNA primer.
See also cDNA.
Reversion
A mutation event that alters an allele conferring a mutant phenotype into one conferring a wild-type phenotype. The mutation need not restore the gene to its original nucleotide sequence to be considered a reversion event.
Revertant
An individual carrying an allele of a given gene that at one time produced a mutant phenotype, but which since has undergone a subsequent mutation that restored a wild-type phenotype. The mutation need not restore the gene to its original nucleotide sequence to be considered a reversion event.
RFLP
Restriction Fragment Length Polymorphism. A genetic polymorphism with respect to the observed length of a restriction fragment. RFLPs can result from single nucleotide polymorphisms as well as from insertions, deletions, or microsatellite expansions.
Ribosome
A complex of proteins and RNA within which translation is carried out.
Ribozyme
An RNA molecule with catalytic activity.
RNA
Ribonucleic acid. A nucleic acid that is the primary product of gene expression. Chemically, it differs from DNA by the substitution of ribose for deoxyribose in the sugar-phosphate backbone and by the substitution of the base uracil for thymine. See the Figure at NHGRI.
See also:
RNA Editing
The alteration of the sequence of an RNA molecule by enyzmatic modification of individual bases without normal splicing.
RNA Gene
A gene whose product is an RNA.
RNA Polymerase
An enzyme that carries out transcription.
RNA Processing
Modifications to an RNA molecule after transcription, including splicing, polyadenylation, and editing.
RNAse
Ribonuclease. A protein that cleaves the phosphodiester backbone of RNA enzymatically.
RNAse Protection
A method of detecting the presence of a specific RNA in a sample. A radioactively-labeled RNA probe is prepared by transcribing the antisense strand of a DNA construct. The labeled probe is hybridized to the sample. The sample is then treated with RNAse, which is specific to single-stranded RNA. The sample is then subjected to electrophoresis and autoradiography. The presence of full-length probe that has not been cleaved by RNAse indicates the presence of the sense strand, and hence gene expression, in the sample.
Robertsonian Translocation
A particular type of translocation in which the breakpoints in the two chromosomes occur at or near the centromere, followed by centric fusion such that the long arms now form a metacentric chromosome with a single centromere. Any small fragments generated in the exchange are usually lost.
See also Translocation.
rRNA
Ribosomal RNA. The RNA molecules that are a structural and catalytic component of the ribosome.
RT-PCR
Reverse-Transcription PCR. A method of amplifying mRNA by first synthesizing cDNA with reverse transcriptase, then amplifying the cDNA using PCR. A positive result is evidence of a particular mRNA, and hence of gene expression, in a sample.
SAM Output File
The Omics Viewer can import gene expression data from a spreadsheet generated by the SAM (Significance Analysis of Microarrays) Microsoft Excel plug-in. This package combines multiple expression experiments to produce a list of statistically significant positively and negatively regulated genes. The Omics Viewer displays the positively regulated genes in one color, and the negatively regulated genes in another color.
SAQP: Structured Advanced Query Page
The SAQP is a graphical user interface to formulate a query to a PGDB without knowing the underlying query language (BioVelo).
Schema
  1. An underlying organizational pattern or structure; conceptual framework.
  2. A collection of items that model part or all of a real world object, particularly in the context of a database, i.e., a database schema.
  3. The structure of a database system, described in a formal language supported by the database management system (DBMS). In a relational database, the schema defines the tables, the fields in each table, and the relationships between fields and tables. Schemas are generally stored in a data dictionary. Although a schema is defined in text database language, the term is often used to refer to a graphical depiction of the database structure.
  4. In computer science, a description of the logical organization, structure, and content of a database.
Secondary_Metabolism
Secondary metabolism is the metabolism of secondary compounds, defined simply as compounds other than primary compounds. A compound is classified as a secondary metabolite if it does not seem to directly function in the processes of growth and development. Even though secondary compounds are a normal part of the metabolism of an organism, they are often produced in specialized cells, and tend to be more complex than primary compounds. Examples of secondary compounds include antibiotics, and plant chemical defenses such as alkaloids and steroids.
Segregation
  1. The separation of homologous chromosomes during meiosis.
  2. The separation of different alleles of the same gene during meiosis.
Semidominant
One of a series of terms applied to the phenotypic effect of a particular allele in reference to another allele (usually the standard wild-type allele) with respect to a given trait. An allele "A" is said to be semidominant with respect to the allele "a" if the A/A homozygote has a mutant phenotype, the A/a heterozygote has a less severe phenotype, while the a/a homozygote is wild-type. An example is Pmp22(Tr-J) in mouse. Pmp22(Tr-J)/Pmp22(Tr-J) animals display a myelination defect associated with a "trembler" phenotype, while Pmp22(Tr-J)/Pmp22(+) animals are less severely affected, and Pmp22(+)/Pmp22(+) animals are wild-type.
See also:
Sense
  1. In molecular biology, that strand of a DNA molecule whose sequence is represented in mRNA.
  2. In molecular biology, an RNA molecule normally processed into mRNA and translated (rather than the complementary sequence).
Sequence
In MGI, a series of nucleotides in RNA or DNA molecules or of amino acids in a protein.
Sequence Annotation
  1. n. Additional information added to genomic sequence to identify genes, delimit the intron and exon structures of those genes, identify regulatory elements, note the positions of allelic variation, etc.
  2. v. The analysis process used to create sequence annotations. The process relies heavily on the homology principle, whereby similarity to known genes is used to help identify new genes and propose functions for them.
Sequence ID (SeqID)
Sequence accession identifier. A unique alphanumeric character string that unambiguously identifies a sequence record in a database. Examples of genomic sequence providers are NCBI and Ensembl; examples of sequence IDs from these providers are 16590 and ENSMUSG00000053869, respectively.
See also:
Sequence Provider
Whole genome sequencing data from large-scale genome projects. Examples of sequence providers used in BioCyc include NCBI and the Comprehensive Microbial Resource (CMR).
See also:
Sequencing
Determination of the order of nucleotides (base sequences) in a DNA or RNA molecule or the order of amino acids in a protein.
Sex Chromosome
Either of two chromosomes that are sexually dimorphic in species with chromosomal (as opposed to genic) sex determination. In mammals, males are the heterogametic sex, having an X chromosome and a Y chromosome, while females are the homogametic sex, having two X chromosomes.
Sex Linked
Located on the X chromosome or the Y chromosome.
Shotgun Sequencing
The sequencing of a large DNA segment through the sequencing of randomly-derived subsegments whose order and orientation within the large segment is unknown until the assembly of overlapping sequences. The method works if all positions in the large segment are covered by multiple overlapping subsegments.
See also Whole-genome shotgun sequencing.
Siibling
This term refers to terms in a hierarchical controlled vocabulary such as those containing Gene Ontology (GO) terms. A "sibling" of a term is a term at the same level of the hierarchy sharing at least one ancestor. For example, the GO term alcohol dehydrogenase [GO:0004022] is a sibling to the GO term aldehyde oxidase [GO:0004031]; they share the ancestor term enzyme [GO:0003824].

See also:
Sigma Factor
A protein component of RNA polymerase that determines the specific site on DNA where transcription begins.
Signal transduction pathway
Pathways that describe the chain of events, such as protein phosphorylation, that occurs during the propagation of a signal in a cell. These pathways start with the binding of ligand by a trans-membrane receptor, and proceed through a series of intermediate molecules until final regulatory molecules, such as transcription factors, are modified in response.
Similarity
In comparison of nucleic acid sequences, the extent to which two nucleic acid sequences have identical bases at equivalent positions, usually expressed as a percentage.
  • In comparison of protein sequences, the extent to which the amino acid sequences of two proteins have identical or functionally similar amino acids at equivalent positions, usually expressed as a percentage.

    • See also Identity.
    Simple Genotype
    A genotype involving a single allele pair.
    Simple-Reactions
    An instance of this Pathway Tools ontology class should be a single reaction involving only a small number of defined participants.
    Simple Sequence Repeat (SSR)
    A sequence consisting largely of a tandem repeat of a specific k-mer (such as (CA)15). Many SSRs are polymorphic and have been widely used in genetic mapping.
    Site-specific Recombination
    Reciprocal recombination between specific target sequences catalyzed by a specific recombination enzyme, as opposed to general homologous recombination. One example is recombination at loxP sites catalyzed by Cre recombinase.
    SMILES
    A language for writing chemical structures in terms of character strings [1]. The chemical substructure searcher within Pathway Tools accepts substructures in the SMILES language.
    SNP
    Single Nucleotide Polymorphism. A type of polymorphism in which two chromosomes differ in a given segment by the identity of a single base pair.
    Solving Mode (MetaFlux)
    This mode of MetaFlux determines the correct fluxes of reactions given a set of nutrients, secretions, and biomass metabolites to produce a feasible FBA Model.
    Somatic
    Cells in an animal other than those that constitute the germ line.
    Somatic Cell Hybrid
    A type of mapping experiment permitting the assignment of markers to chromosomes. The method consists of fusing cultured cells of one species with cultured cells of a different species. The hybrid cells are unstable in karyotype during growth, with most chromosomes from one species typically being lost. Among clonal populations of hybrid cells following growth, different chromosomes are retained from one species. A panel of hybrid cell cultures can be assayed for which mouse chromosomes (for example) are retained, and simultaneously assayed for the presence of particular markers. The correlation of the presence of a particular marker across the panel with the presence of a particular mouse chromosome allows that marker to be assigned to that chromosome.
    See also Radiation Hybrid Mapping.
    Southern Blot
    An assay that detects specific DNA molecules using a DNA or RNA probe with sequence similarity. Samples are subjected to electrophoresis on a slab gel. A replica of the gel is then made on a membrane by capillary transfer following denaturation. Specific DNA sequences are then detected on the membrane with a radioactively- or chemically-labeled probe. See the Figure from Alberts, et al., Molecular Biology of the Cell.
    See also:
    Spindle
    The cellular apparatus that directs chromosome movement during cell division in mitosis or meiosis. The spindle is largely composed of microtubules. See the Figure at NHGRI.
    Splice Acceptor Site
    In the splicing of RNA, the site at the 3' end of an intron.
    See also Splice Donor Site.
    Splice Donor Site
    In the splicing of RNA, the site at the 5' end of an intron.
    See also Splice Acceptor Site.
    Splice Junction
    In the splicing of RNA, the site of a former intron in a mature mRNA.
    Splicing
    Part of the processing of an RNA transcript into mRNA, in which introns are removed enzymatically.
    Spontaneous
    As a type of mutation, one that has occurred in the absence of any experimental mutagenic treatment, such as irradiation or treatment with chemical mutagens.
    SQL
    Structured Query Language. SQL is used to communicate with a database. According to ANSI (American National Standards Institute), it is the standard language for relational database management systems. SQL statements perform tasks such as updating data in or retrieving data from a database. Some common relational database management systems that use SQL are: Oracle, Sybase, Microsoft SQL Server, Access, Ingres, etc. Although most database systems use SQL, most of them also have their own additional proprietary extensions that are usually only used on their system.
    SSLP
    Simple Sequence Length Polymorphism, a type of polymorphism that results from variation in the length of an SSR.
    SSR
    Simple Sequence Repeat, a DNA sequence consisting largely of a tandem repeat of a specific k-mer (such as (CA)15). Many SSRs are polymorphic and have been widely used in genetic mapping.
    Stop Codon
    One of three codons that signal that translation of an RNA sequence should cease.
    Strain
    Strain is a low-level taxonomic rank used in three related ways. In Microbiology, a strain is a genetic variant or subtype of a microorganism (e.g. virus or bacterium or fungus). In plants, a strain is a designated group of offspring that have descended from a modified plant, produced either by conventional breeding or by biotechnological means or result from genetic mutation. In rodents, a strain is a group of animals that is genetically uniform.
    Structural Gene
    A gene that encodes an enzyme or structural protein, in contrast to a regulatory gene.
    Structural Protein
    A protein that functions as a structural element of cells rather than as an enzyme, for example, collagen.
    Structured Data
    Structured data are data that have been represented in a manner that allows computation with those data. Data become structured when they are carefully dissected and assigned to distinct fields of a database with clearly defined meanings, so that the data are independently queryable and computable. Therefore, we can ask questions across the data such as "find all enzymes that use magnesium as a cofactor" or "find all pathways in which pyruvate is an input substrate". See also Unstructured Data.
    Structured Query Language
    Structured Query Language (SQL) is used to communicate with a database. According to ANSI (American National Standards Institute), it is the standard language for relational database management systems. SQL statements perform tasks such as updating data in or retrieving data from a database. Some common relational database management systems that use SQL are: Oracle, Sybase, Microsoft SQL Server, Access, Ingres, etc. Although most database systems use SQL, most of them also have their own additional proprietary extensions that are usually only used on their system. The Query Forms at MGI extract information from databases by generating instructions in SQL.
    STS
    Sequence Tagged Site. A short segment of unique sequence derived from genomic DNA. A large collection of STSs can be used to assemble a physical map of the genome from a collection of genomic clones (e.g., BACs or YACs) by testing each clone for the presence of each STS. Two clones that contain one or more STSs in common must overlap. For examples, see the physical maps of the mouse genome at MGI.
    Subpathway
    See Superpathway
    Substrate
    A molecule acted upon by an enzyme.
    Superpathway
    Superpathways are a class of PGDB metabolic pathways that are constructed by combining and connecting individual pathways (which can be shown separately) to depict relationships between them. In some cases those individual pathways start from a common precursor, or produce a common product, but they can have other relationships as well. Superpathways can have individual reactions as their components in addition to other pathways. Superpathways can be defined recursively, that is, the component pathway of a Superpathway can be a base pathway or can itself be a superpathway. Most superpathways will have an additional parent class within the pathway ontology to define their biological role.
    SWISS-PROT
    A curated protein sequence database. See the SWISS-PROT site for more details.
    Synonym
    A synonym is one of several names that are, or have been used, in the scientific literature or in public databases to refer to one object. For example, 2-phosphoglyceric acid, 2-PGA, and glycerate 2-phosphate are all synonyms of the compound 2-phosphoglycerate. In BioCyc, one of the synonyms is designated as the common name
    Synteny
    The state of being on the same chromosome. A gene is also said to be syntenic to a particular chromosome if it is known to be located on that chromosome but is otherwise unmapped.
    See also Conserved Synteny.
    System Catalog
    The data dictionary of a DBMS. The system catalog stores metadata including the schemas of the databases. It is a mini-database, and is usually stored using the DBMS itself in special tables called system tables. It maybe referred to as being "on line", as it is active, and users can query it like any other table.
    Tab-delimited file
    A text file that uses tabs to separate adjacent fields. It is a common format for downloading information into a spreadsheet.
    Table
    Refers to data arranged in rows and columns. A spreadsheet, for example, is a table. In relational databases, all information is stored in the form of tables.
    Targeted Mutation
    A type of mutation in which a chromosomal gene is altered by the substitution of a DNA construct assembled in vitro. The constructs are usually designed to eliminate gene function; such targeted mutations are often casually referred to as knock outs. Some DNA constructs are designed to alter gene function; such targeted mutations are often casually referred to as knock ins.
    Telomere
    A specialized structure at the ends of linear chromosomes in eukaryotes. Telomeres confer stability on chromosome ends. Chromosome ends lacking telomeres, such as those generated from interstitial sites by chromosome breaks, are reactive, often fusing with other broken ends to generate chromosome rearrangements. Telomeres also permit the ends of linear chromosomes to replicate fully. See the Figure at NHGRI.
    Template
    In the process of replication or transcription, the strand of DNA that serves as the source of information.
    Termination Codon
    One of three codons that signal that translation of an RNA sequence should cease.
    Terminator
    A DNA sequence that signals the end of transcription.
    Testcross
    A type of cross in which individuals whose genotype with respect to one or more genes is unknown are crossed to a test strain homozygous for a recessive allele at the genes under study. For example, a cross of an individual that was A/A or A/a (identical in phenotype) to a/a would reveal the genotype of the individual being tested, because if the individual being tested were A/A, all of the progeny would show the dominant phenotype, while if the individual being tested were A/a, half of the progeny would show the dominant phenotype and half would show the recessive phenotype.
    See also:
    Thermostable
    Used to describe an enzyme or other protein that is not denatured at temperatures that denature most other proteins.
    Thymine (T)
    A pyrimidine base that is a component of nucleotides and thus a normal component of DNA. Uracil replaces thymine in RNA. See the Figure at NHGRI.
    Trait
    A particular aspect of the phenotype that can be measured or observed directly, e.g., blood pressure or body weight.
    Transcript
    An RNA molecule (or species of RNA molecule) that is the product of transcription.
    Transcription
    The enzymatic synthesis of an RNA molecule directed by information in a DNA molecule. See the Figure at NHGRI.
    See also Central Dogma.
    Transcription Start
    The location at the 5′ end of a gene, adjacent to the promoter, at which the RNA polymerase complex binds to the DNA and initiates the process of transcription of that gene into mRNA. The precise context of the TSS depends on the gene, its host organism, the type of polymerase involved, and other factors.
    Transcription Unit
    A transcription unit is a sequence of nucleotides in DNA that codes for a single RNA molecule, along with the sequences necessary for its transcription; normally a transcription unit contains a promoter, an RNA-coding sequence, and a terminator. Similar to operons, however, operons containing multiple promoters and/or terminators correspond to multiple transcription units.
    Transgene
    Any DNA sequence or combination of sequences that has been introduced via a construct into the germ line of the animal by random integration.
    Transgenic mouse
    A mouse that contains a stably inherited DNA which has been inserted randomly into the genome. The inserted gene sequence (the transgene) may or may not be derived from mouse sequence.
    Transition
    A type of point mutation in which a purine is substituted for another purine or a pyrimidine for another pyrimidine. These substitutions include A for G, G for A, C for T, or T for C.
    See also Transversion.
    Translation
    The enzymatic synthesis of a protein molecule directed by the information in an mRNA molecule. The mRNA is read from the 5' end to the 3' end, with the protein being synthesized from the amino terminus to the carboxyl terminus. See the Figure at Access Excellence or the Figure at NHGRI.
    See also Central Dogma.
    Translocation
    A type of mutation in which two nonhomologous chromosomes are each broken and then repaired in such a way that:
    1. the resulting chromosomes each contain material from the other chromosome (areciprocal translocation), see the Figure at NHGRI)
    2. one of the chromosomes contains an insertion of material from the other chromosome, with the other chromosome containing a deletion (an insertional translocation, see the Figure at NHGRI) or
    3. the two chromosomes, each with breaks near the centromere, fuse to form a single chromosome with a single centromere (a Robertsonian translocation).
    Transport-Reactions
    This Pathway Tools ontology class defines reactions in which at least one species is transported (passively or actively) across a membrane. The species may or may not be chemically modified in the course of the reaction. A transport reaction is assumed to occur physiologically in the direction written; if it proceeds in the reverse direction, this fact should be indicated in the enzymatic-reaction for a given transporter.
    Transposition
    1. A type of chromosome rearrangement in which a segment of a chromosome is moved to a different location on the same chromosome, resembling an insertional translocation involving a single chromosome.
    2. The movement of a mobile genetic element to a new location.
    Transposon
    A type of mobile genetic element consisting of DNA that moves to new genomic locations conservatively (without replicating itself) or replicatively (moving a copy of itself).
    Transversion
    A type of point mutation in which a purine is substituted for a pyrimidine or a pyrimidine for a purine. These substitutions include C or T for A, C or T for G, A or G for C, and A or G for T.
    See also Transition.
    TrEMBL
    A protein sequence database that contains all the translations of EMBL nucleotide sequences. See the TrEMBL site for more details.
    Trisomy
    The condition of having three chromosomes of a particular type. Down Syndrome in humans is a trisomy for chromosome 21.
    See also Monosomy.
    tRNA
    Transfer RNA. Small RNA molecules that bind to the codons of mRNA in the ribosome after being "charged" with amino acids.
    Try Set
    A try-set is a mechanism used within the Pathway Tools MetaFlux module to allow MetaFlux to explore potential modifications to an FBA model. A try-set defines a set of reactions or metabolites that can be added to a base model that is considered incomplete. Try-sets can be specified for reactions, nutrients, secretions, and biomass metabolites.
    UniGene
    An experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters. Each UniGene cluster contains sequences that represent a unique gene, as well as related information such as the tissue types in which the gene has been expressed and map location. See the UniGene page at NCBI.
    Uniparental Disomy
    The inheritance, in a diploid organism, of both copies of a single chromosome from one parent. This may result from the union of a gamete bearing two copies of one chromosome with a gamete bearing no copy of that chromosome, or from the union of a gamete bearing two copies of one chromosome with a normal gamete, followed by the loss of one chromosome through an error in mitosis. Because of imprinting, uniparental disomy can have phenotypic consequences in mammals. See, for example, Prader-Willi Syndrome.
    Unstructured Data
    Data which is not structured, such as the free-text comments within a database. Such comments are not structured because the computer cannot compute with the data. Computers cannot read text, therefore they cannot extract individual data elements from large text blocks such that the meanings of those data elements are reliably known. See also Structured Data.
    Uracil (U)
    A pyrimidine base that is a componentof nucleotides and thus a normal component of RNA. Thymine replaces uracil in DNA. See the Figure at NHGRI.
    URL
    Uniform Resource Locator. An Internet address giving the protocol to be used for obtaining resources on the Internet such as "ftp:" for an FTP site or "http:" for a World Wide Web page. It also includes the server name and sometimes the path to the resource. The URL for BioCyc is "http://www.biocyc.org" target="_blank".
    Vector
    See Cloning Vector.
    VEGA
    Vertebrate Genome Annotation. The VEGA database is a central repository for high quality, frequently updated, manual annotation of vertebrate finished genome sequence. VEGA developed within Ensembl as a joint project between EMBL-EBI and the Sanger Institute.
    Virus
    A noncellular biological entity that requires a host cell for reproduction. Viruses consist of a nucleic acid genome that is either DNA or, in the case of retroviruses, RNA. The viral genome is covered with a protein coat; some viruses have a host-derived membrane over the protein coat.
    VISTA
    A suite of programs and databases for comparative analysis of genomic sequences. Users can either submit sequences and alignments for analysis or examine precomputed whole-genome alignments of different species. See http://genome.lbl.gov/vista/index.shtml.
    Western Blot
    An assay that detects specific proteins within a protein mixture. Samples are subjected to electrophoresis on a slab gel. A replica of the gel is then made on a membrane by electrophoretic transfer. Specific proteins are then detected on the membrane using antibody staining.
    See also:
    Whole-genome Shotgun Sequencing
    The sequencing of the entire genome of an organism through the sequencing of randomly-derived subsegments whose order and orientation is unknown until the assembly of overlapping sequences is performed computationally. The method works if all positions in the genome are covered by multiple overlapping subsegments.
    See also:
    Wild Type
    1. The phenotype with respect to a given inherited characteristic that is considered to be the "normal" type commonly found in natural populations.
    2. The allele of a particular gene that confers the phenotype considered to be the "normal" type commonly found in natural populations. N.B.: Because some DNA sequence polymorphisms do not produce different phenotypes, there can be multiple "wild-type" alleles of a gene.
    Wild Type Allele
    One of many possible versions of a gene that functions normally, as opposed to versions of a gene that are functionally abnormal (i.e., mutant alleles).
    Withdrawn
    With respect to gene nomenclature, a withdrawn symbol name was once the approved symbol or name for a marker; there is currently a different approved symbol or name for that marker.
    X Chromosome
    One of pair of chromosomes that is sexually dimorphic in mammals. Normal female mammals have two X chromosomes, while normal male mammals have an X chromosome and a Y chromosome.
    X Inactivation
    The condensation of all but one of the X chromosomes of a mammal into a heterochromatic state, eliminating gene expression from all but the active X chromosome. This process ensures that male and female mammals have the same level of gene activity of X-chromosome genes.
    YAC
    Yeast Artificial Chromosome.
    Y Chromosome
    One of pair of chromosomes that is sexually dimorphic in mammals. Normal female mammals have two X chromosomes, while normal male mammals have an X chromosome and a Y chromosome.

    BioCyc gratefully acknowledges the use of the glossary at Mouse Genome Informatics as the basis for this glossary.