Abstract
The Gene Expression Omnibus (GEO) database is a major repository that stores high-throughput functional genomics data sets that are generated using both microarray-based and sequence-based technologies. Data sets are submitted to GEO primarily by researchers who are publishing their results in journals that require original data to be made freely available for review and analysis. In addition to serving as a public archive for these data, GEO has a suite of tools that allow users to identify, analyze, and visualize data relevant to their specific interests. These tools include sample comparison applications, gene expression profile charts, data set clusters, genome browser tracks, and a powerful search engine that enables users to construct complex queries.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Edgar R, Domrachev M, Lash AE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30:207–210
Barrett T, Troup DB, Wilhite SE et al (2009) NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res 37:D885–890
Sayers EW, Barrett T, Benson DA et al (2009) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 37:D5–15
Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Fingerman IM, McDaniel L, Zhang X et al (2011) NCBI Epigenomics: A new public resource for exploring epigenomic datasets. Nucleic Acids Res 39:D908–12
Rhead B, Karolchik D, Kuhn RM et al (2010) The UCSC Genome Browser database: update 2010. Nucleic Acids Res 38:D613–619.
Bhattacharya A, De RK (2008) Divisive Correlation Clustering Algorithm (DCCA) for grouping of genes: detecting varying patterns in expression profiles. Bioinformatics 24:1359–1366
Pierre M, DeHertogh B, Gaigneaux A et al (2010) Meta-analysis of archived DNA microarrays identifies genes regulated by hypoxia and involved in a metastatic phenotype in cancer cells. BMC Cancer 10:176
Ogata Y, Suzuki H, Sakurai N et al (2010) CoP: a database for characterizing co-expressed gene modules with biological information in plants. Bioinformatics 26:1267–1268
Liu S (2010) Increasing alternative promoter repertories is positively associated with differential expression and disease susceptibility. PLoS One 5:e9482
Chen R, Sigdel TK, Li L et al (2010) Differentially Expressed RNA from Public Microarray Data Identifies Serum Protein Biomarkers for Cross-Organ Transplant Rejection and Other Conditions. PLoS Comput Biol 6:e1000940
http://www.nlm.nih.gov/pubs/techbull/jf05/jf05_myncbi.html#register
McGrath-Morrow S, Rangasamy T, Cho C et al (2008) Impaired lung homeostasis in neonatal mice exposed to cigarette smoke. Am J Respir Cell Mol Biol 38:393–400
Acknowledgments
This chapter is an official contribution of the National Institutes of Health; not subject to copyright in the USA. The authors unreservedly acknowledge the expertise of the whole GEO curation and development team – Pierre Ledoux, Carlos Evangelista, Irene Kim, Kimberly Marshall, Katherine Phillippy, Patti Sherman, Michelle Holko, Dennis Troup, Maxim Tomashevsky, Rolf Muertter, Oluwabukunmi Ayanbule, Andrey Yefanov, and Alexandra Soboleva.
Funding
This research was supported by the Intramural Research Program of the NIH, National Library of Medicine.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Wilhite, S.E., Barrett, T. (2012). Strategies to Explore Functional Genomics Data Sets in NCBI’s GEO Database. In: Wang, J., Tan, A., Tian, T. (eds) Next Generation Microarray Bioinformatics. Methods in Molecular Biology, vol 802. Humana Press. https://doi.org/10.1007/978-1-61779-400-1_3
Download citation
DOI: https://doi.org/10.1007/978-1-61779-400-1_3
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-61779-399-8
Online ISBN: 978-1-61779-400-1
eBook Packages: Springer Protocols