Reuse of public genome-wide gene expression data.

Rung J; Brazma A

doi:10.1038/nrg3394

Reuse of public genome-wide gene expression data.

Rung J ¹,

Brazma A

Affiliations

1. EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Authors
Rung J¹
(1 author)

ORCIDs linked to this article

Nature reviews. Genetics, 27 Dec 2012, 14(2):89-99
https://doi.org/10.1038/nrg3394 PMID: 23269463

Review

Abstract

Our understanding of gene expression has changed dramatically over the past decade, largely catalysed by technological developments. High-throughput experiments - microarrays and next-generation sequencing - have generated large amounts of genome-wide gene expression data that are collected in public archives. Added-value databases process, analyse and annotate these data further to make them accessible to every biologist. In this Review, we discuss the utility of the gene expression data that are in the public domain and how researchers are making use of these data. Reuse of public data can be very powerful, but there are many obstacles in data preparation and analysis and in the interpretation of the results. We will discuss these challenges and provide recommendations that we believe can improve the utility of such data.

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Read article at publisher's site: https://doi.org/10.1038/nrg3394

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Funding

Funders who supported this work.

Biotechnology and Biological Sciences Research Council (1)

Development of integrated web interfaces for Bioconductor genomic data analysis, annotation and visualization tools
Dr Alvis Brazma, EMBL - European Bioinformatics Institute
Grant ID: BB/E001653/1
7 publications

Search life-sciences literature (45,105,671 articles, preprints and more)

Reuse of public genome-wide gene expression data.

Affiliations

Authors

ORCIDs linked to this article

Abstract

Full text links

References

Quantitative monitoring of gene expression patterns with a complementary DNA microarray.

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Bioconductor: open software development for computational biology and bioinformatics.

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.

ArrayExpress--a public repository for microarray gene expression data at the EBI.

RNA-Seq: a revolutionary tool for transcriptomics.

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments.

NCBI GEO: archive for functional genomics data sets--10 years on.

The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments.

Citations & impact

Impact metrics

Citations of article over time

Alternative metrics

Article citations

Transcriptome meta-analysis and validation to discovery of hub genes and pathways in focal and segmental glomerulosclerosis.

Identification of genes predicting chemoresistance and short survival in ovarian cancer.

Transcriptomics analysis highlights potential ways in human pathogenesis in Leishmania braziliensis infected with the viral endosymbiont LRV1.

Integrated meta-analysis of colorectal cancer public proteomic datasets for biomarker discovery and validation.

Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences.

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Funding

Biotechnology and Biological Sciences Research Council (1)

Development of integrated web interfaces for Bioconductor genomic data analysis, annotation and visualization tools

Partnerships & funding

Search life-sciences literature (45,105,671 articles, preprints and more)

Reuse of public genome-wide gene expression data.

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Affiliations

Authors

ORCIDs linked to this article

Abstract

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References

Citations & impact

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Funding

Biotechnology and Biological Sciences Research Council (1)﻿

Partnerships & funding

Biotechnology and Biological Sciences Research Council (1)