NCBI Epigenomics: Difference between revisions
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The '''Epigenomic Database''' of the [[National Center for Biotechnology Information]] (NCBI) at the [[National Institutes of Health]] (NIH) was launched in June 2010 as a means to collect maps of epigenetic modifications and their occurrence across the human genome.<ref>{{cite web|title=Overview|url=https://commonfund.nih.gov/epigenomics/overview.aspx|work=National Institutes of Health|publisher=Office of Strategic Coordination- The Common Fund|accessdate=22 September 2013}}</ref> This database provides a publicly available resource for maps in [[stem cells]] and primary ''ex vivo'' tissues that detail genome-wide landscapes of epigenetic factors that occur in human development and disease.<ref name="pmid21075792">{{cite journal | quotes = yes|last=Fingerman|first=Ian M|authorlink=|coauthors=McDaniel Lee, Zhang Xuan, Ratzat Walter, Hassan Tarek, Jiang Zhifang, Cohen Robert F, Schuler Gregory D|year=2011|month=Jan|title=NCBI Epigenomics: a new public resource for exploring epigenomic data sets|journal = Nucleic Acids Res.|volume=39|issue=Database issue|pages=D908-12|publisher= |location = England| issn = | pmid = 21075792|doi = 10.1093/nar/gkq1146| bibcode = | oclc =| id = | url = | pmc =3013719 |language = eng| format = | accessdate = | laysummary = | laysource = | laydate = | quote = }}</ref> |
The '''Epigenomic Database''' of the [[National Center for Biotechnology Information]] (NCBI) at the [[National Institutes of Health]] (NIH) was launched in June 2010 as a means to collect maps of epigenetic modifications and their occurrence across the human genome.<ref>{{cite web|title=Overview|url=https://commonfund.nih.gov/epigenomics/overview.aspx|work=National Institutes of Health|publisher=Office of Strategic Coordination- The Common Fund|accessdate=22 September 2013}}</ref> This database provides a publicly available resource for maps in [[stem cells]] and primary ''ex vivo'' tissues that detail genome-wide landscapes of epigenetic factors that occur in human development and disease.<ref name="pmid21075792">{{cite journal | quotes = yes|last=Fingerman|first=Ian M|authorlink=|coauthors=McDaniel Lee, Zhang Xuan, Ratzat Walter, Hassan Tarek, Jiang Zhifang, Cohen Robert F, Schuler Gregory D|year=2011|month=Jan|title=NCBI Epigenomics: a new public resource for exploring epigenomic data sets|journal = Nucleic Acids Res.|volume=39|issue=Database issue|pages=D908-12|publisher= |location = England| issn = | pmid = 21075792|doi = 10.1093/nar/gkq1146| bibcode = | oclc =| id = | url = | pmc =3013719 |language = eng| format = | accessdate = | laysummary = | laysource = | laydate = | quote = }}</ref> |
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===Content of Epigenomics database=== |
===Content of Epigenomics database=== |
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The primary resources for the content of the Epigenomics Database are derived from two archival databases at the NCBI: The Gene Expression Omnibus (GEO) and the Sequence Read Archive (SRA). <ref name="pmid21075792">{{cite journal | quotes = yes|last=Fingerman|first=Ian M|authorlink=|coauthors=McDaniel Lee, Zhang Xuan, Ratzat Walter, Hassan Tarek, Jiang Zhifang, Cohen Robert F, Schuler Gregory D|year=2011|month=Jan|title=NCBI Epigenomics: a new public resource for exploring epigenomic data sets|journal = Nucleic Acids Res.|volume=39|issue=Database issue|pages=D908-12|publisher= |location = England| issn = | pmid = 21075792|doi = 10.1093/nar/gkq1146| bibcode = | oclc =| id = | url = | pmc =3013719 |language = eng| format = | accessdate = | laysummary = | laysource = | laydate = | quote = }}</ref> |
The primary resources for the content of the Epigenomics Database are derived from two archival databases at the NCBI: The Gene Expression Omnibus (GEO) and the Sequence Read Archive (SRA).<ref name="pmid21075792">{{cite journal | quotes = yes|last=Fingerman|first=Ian M|authorlink=|coauthors=McDaniel Lee, Zhang Xuan, Ratzat Walter, Hassan Tarek, Jiang Zhifang, Cohen Robert F, Schuler Gregory D|year=2011|month=Jan|title=NCBI Epigenomics: a new public resource for exploring epigenomic data sets|journal = Nucleic Acids Res.|volume=39|issue=Database issue|pages=D908-12|publisher= |location = England| issn = | pmid = 21075792|doi = 10.1093/nar/gkq1146| bibcode = | oclc =| id = | url = | pmc =3013719 |language = eng| format = | accessdate = | laysummary = | laysource = | laydate = | quote = }}</ref> The Gene Expression Omnibus is a data system for high-throughput genomic data that is generated from microarray and next-generation sequencing technologies.<ref>{{cite journal|last=Sayers|first=EW|coauthors=Et. al|title=Database resources of the National Center for Biotechnology Information.|journal=Nucleic Acids Research|year=2010|month=January|volume=38|page=D5–D16|doi=10.1093/nar/gkp967|pmid=19910364|url=http://www.ncbi.nlm.nih.gov/pubmed/19910364|accessdate=20 October 2013}}</ref> Data used in the Epigenomics database is a combination of GEO and SRA subsets that are specific to Epigenetic factors. This data is subjected to additional review and organized in a more easily attainable fashion before added to the Epigenomics database. <ref name="pmid21075792">{{cite journal | quotes = yes|last=Fingerman|first=Ian M|authorlink=|coauthors=McDaniel Lee, Zhang Xuan, Ratzat Walter, Hassan Tarek, Jiang Zhifang, Cohen Robert F, Schuler Gregory D|year=2011|month=Jan|title=NCBI Epigenomics: a new public resource for exploring epigenomic data sets|journal = Nucleic Acids Res.|volume=39|issue=Database issue|pages=D908-12|publisher= |location = England| issn = | pmid = 21075792|doi = 10.1093/nar/gkq1146| bibcode = | oclc =| id = | url = | pmc =3013719 |language = eng| format = | accessdate = | laysummary = | laysource = | laydate = | quote = }}</ref> |
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==Roadmap Epigenomics Project== |
==Roadmap Epigenomics Project== |
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In 2007 the [[National Institutes of Health]] (NIH) launched the '''Roadmap Epigenomics Project'''. The aim of the project is a development of publicly available reference epigenome maps from a variety of cell types.<ref name="pmid21075792">{{cite journal | quotes = yes|last=Fingerman|first=Ian M|authorlink=|coauthors=McDaniel Lee, Zhang Xuan, Ratzat Walter, Hassan Tarek, Jiang Zhifang, Cohen Robert F, Schuler Gregory D|year=2011|month=Jan|title=NCBI Epigenomics: a new public resource for exploring epigenomic data sets|journal = Nucleic Acids Res.|volume=39|issue=Database issue|pages=D908-12|publisher= |location = England| issn = | pmid = 21075792|doi = 10.1093/nar/gkq1146| bibcode = | oclc =| id = | url = | pmc =3013719 |language = eng| format = | accessdate = | laysummary = | laysource = | laydate = | quote = }}</ref> These epigenetic maps are intended to provide resources for studies of epigenetic events that underline human development, diversity, and disease.<ref name=pmid20944595>{{cite journal|last=Bernstein|first=Bradley E|coauthors=Bradley E Bernstein, John A Stamatoyannopoulos, Joseph F Costello, Bing Ren, Aleksandar Milosavljevic, Alexander Meissner, Manolis Kellis, Marco A Marra, Arthur L Beaudet, Joseph R Ecker, Peggy J Farnham, Martin Hirst, Eric S Lander, Tarjei S Mikkelsen & James A Thomson|title=The NIH Roadmap Epigenomics Mapping Consortium|journal=Nature Biotechnology|date=13|year=2010|month=October|volume=28|page=1045-1048|doi=10.1038/nbt1010-1045|pmid=20944595|url=http://www.nature.com/nbt/journal/v28/n10/full/nbt1010-1045.html|accessdate=22 September 2013}}</ref> For similar efforts see the [[ENCODE]](ENCyclopedia Of DNA Elements) Project, whose initiatives are complementary to the Roadmap Epigenomics Project.<ref name=pmid15499007>{{cite journal|title=The ENCODE (ENCyclopedia Of DNA Elements) Project|journal=Science|date=22|year=2004|month=October|volume=306|issue=5696|page=636-40|doi=10.1126/science.1105136|pmid=15499007|url=http://www.ncbi.nlm.nih.gov/pubmed/15499007/|accessdate=22 September 2013}}</ref> |
In 2007 the [[National Institutes of Health]] (NIH) launched the '''Roadmap Epigenomics Project'''. The aim of the project is a development of publicly available reference epigenome maps from a variety of cell types.<ref name="pmid21075792">{{cite journal | quotes = yes|last=Fingerman|first=Ian M|authorlink=|coauthors=McDaniel Lee, Zhang Xuan, Ratzat Walter, Hassan Tarek, Jiang Zhifang, Cohen Robert F, Schuler Gregory D|year=2011|month=Jan|title=NCBI Epigenomics: a new public resource for exploring epigenomic data sets|journal = Nucleic Acids Res.|volume=39|issue=Database issue|pages=D908-12|publisher= |location = England| issn = | pmid = 21075792|doi = 10.1093/nar/gkq1146| bibcode = | oclc =| id = | url = | pmc =3013719 |language = eng| format = | accessdate = | laysummary = | laysource = | laydate = | quote = }}</ref> These epigenetic maps are intended to provide resources for studies of epigenetic events that underline human development, diversity, and disease.<ref name=pmid20944595>{{cite journal|last=Bernstein|first=Bradley E|coauthors=Bradley E Bernstein, John A Stamatoyannopoulos, Joseph F Costello, Bing Ren, Aleksandar Milosavljevic, Alexander Meissner, Manolis Kellis, Marco A Marra, Arthur L Beaudet, Joseph R Ecker, Peggy J Farnham, Martin Hirst, Eric S Lander, Tarjei S Mikkelsen & James A Thomson|title=The NIH Roadmap Epigenomics Mapping Consortium|journal=Nature Biotechnology|date=13|year=2010|month=October|volume=28|page=1045-1048|doi=10.1038/nbt1010-1045|pmid=20944595|url=http://www.nature.com/nbt/journal/v28/n10/full/nbt1010-1045.html|accessdate=22 September 2013}}</ref> For similar efforts see the [[ENCODE]](ENCyclopedia Of DNA Elements) Project, whose initiatives are complementary to the Roadmap Epigenomics Project.<ref name=pmid15499007>{{cite journal|title=The ENCODE (ENCyclopedia Of DNA Elements) Project|journal=Science|date=22|year=2004|month=October|volume=306|issue=5696|page=636-40|doi=10.1126/science.1105136|pmid=15499007|url=http://www.ncbi.nlm.nih.gov/pubmed/15499007/|accessdate=22 September 2013}}</ref> |
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Revision as of 22:49, 20 October 2013
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| Content | |
|---|---|
| Description | epigenomic data sets. |
| Contact | |
| Research center | National Center for Biotechnology Information |
| Authors | Ian M Fingerman |
| Primary citation | Fingerman & al. (2011)[1] |
| Release date | 2010 |
| Access | |
| Website | http://www.ncbi.nlm.nih.gov/epigenomics |
The Epigenomics database at the National Center for Biotechnology Information is a database for whole-genome epigenetics data sets.[1]
The Epigenomics Database
The Epigenomic Database of the National Center for Biotechnology Information (NCBI) at the National Institutes of Health (NIH) was launched in June 2010 as a means to collect maps of epigenetic modifications and their occurrence across the human genome.[2] This database provides a publicly available resource for maps in stem cells and primary ex vivo tissues that detail genome-wide landscapes of epigenetic factors that occur in human development and disease.[1]
Content of Epigenomics database
The primary resources for the content of the Epigenomics Database are derived from two archival databases at the NCBI: The Gene Expression Omnibus (GEO) and the Sequence Read Archive (SRA).[1] The Gene Expression Omnibus is a data system for high-throughput genomic data that is generated from microarray and next-generation sequencing technologies.[3] Data used in the Epigenomics database is a combination of GEO and SRA subsets that are specific to Epigenetic factors. This data is subjected to additional review and organized in a more easily attainable fashion before added to the Epigenomics database. [1]
Roadmap Epigenomics Project
In 2007 the National Institutes of Health (NIH) launched the Roadmap Epigenomics Project. The aim of the project is a development of publicly available reference epigenome maps from a variety of cell types.[1] These epigenetic maps are intended to provide resources for studies of epigenetic events that underline human development, diversity, and disease.[4] For similar efforts see the ENCODE(ENCyclopedia Of DNA Elements) Project, whose initiatives are complementary to the Roadmap Epigenomics Project.[5]
The Epigenome
The epigenome consists of a record of the chemical changes to the DNA and Histone proteins of an organism. These chemical changes influence gene expression across many tissue types and developmental stages.[6] These epigenetic changes involve methods of altering gene expression that do not involve changes in the underlying primary DNA sequence; these include DNA methylation, Gene silencing, and chromatin structure, [7] as well as involvement of Non-coding RNA.[8]
References
- ^ a b c d e f Fingerman, Ian M (2011). "NCBI Epigenomics: a new public resource for exploring epigenomic data sets". Nucleic Acids Res. (in eng). 39 (Database issue). England: D908-12. doi:10.1093/nar/gkq1146. PMC 3013719. PMID 21075792.
{{cite journal}}: Cite has empty unknown parameters:|laydate=,|laysource=, and|laysummary=(help); Unknown parameter|coauthors=ignored (|author=suggested) (help); Unknown parameter|month=ignored (help); Unknown parameter|quotes=ignored (help)CS1 maint: unrecognized language (link) - ^ "Overview". National Institutes of Health. Office of Strategic Coordination- The Common Fund. Retrieved 22 September 2013.
- ^ Sayers, EW (2010). "Database resources of the National Center for Biotechnology Information". Nucleic Acids Research. 38: D5–D16. doi:10.1093/nar/gkp967. PMID 19910364. Retrieved 20 October 2013.
{{cite journal}}: Unknown parameter|coauthors=ignored (|author=suggested) (help); Unknown parameter|month=ignored (help) - ^ Bernstein, Bradley E (13). "The NIH Roadmap Epigenomics Mapping Consortium". Nature Biotechnology. 28: 1045-1048. doi:10.1038/nbt1010-1045. PMID 20944595. Retrieved 22 September 2013.
{{cite journal}}: Check date values in:|date=and|year=/|date=mismatch (help); Unknown parameter|coauthors=ignored (|author=suggested) (help); Unknown parameter|month=ignored (help) - ^ "The ENCODE (ENCyclopedia Of DNA Elements) Project". Science. 306 (5696): 636-40. 22. doi:10.1126/science.1105136. PMID 15499007. Retrieved 22 September 2013.
{{cite journal}}: Check date values in:|date=and|year=/|date=mismatch (help); Unknown parameter|month=ignored (help) - ^ Bernstein, Bradley E (19). "The Mammalian Epigenome". Cell. 4. 128: 669-681. doi:10.1016/j.cell.2007.01.033. PMID 17320505. Retrieved 22 September 2013.
{{cite journal}}: Check date values in:|date=and|year=/|date=mismatch (help); Unknown parameter|coauthors=ignored (|author=suggested) (help); Unknown parameter|month=ignored (help) - ^ Russo, Vincenzo EA, Robert A. Martienssen, and Arthur D. Riggs. (1996). Epigenetic Mechanisms of Gene Regulation. Cold Spring Harbor Laboratory Press. p. Abstract. ISBN 0-87969-490-4.
{{cite book}}: CS1 maint: multiple names: authors list (link) - ^ Costa, Fabricio F. (29). "Non-coding RNAs, epigenetics and complexity". Gene. 410 (1): 9-17. doi:10.1016/j.gene.2007.12.008. PMID 18226475. Retrieved 22 September 2013.
{{cite journal}}: Check date values in:|year=,|date=, and|year=/|date=mismatch (help); Unknown parameter|month=ignored (help)CS1 maint: year (link)
See also
External links
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