Review
doi: 10.1093/bib/bbn001.
Epub 2008 Jan 17.
Gene-set approach for expression pattern analysis
Affiliations
- PMID: 18202032
- DOI: 10.1093/bib/bbn001
Item in Clipboard
Review
Gene-set approach for expression pattern analysis
Brief Bioinform.
2008 May.
Erratum in
- Brief Bioinform. 2008 Sep;9(5):450
Abstract
Recently developed gene set analysis methods evaluate differential expression patterns of gene groups instead of those of individual genes. This approach especially targets gene groups whose constituents show subtle but coordinated expression changes, which might not be detected by the usual individual gene analysis. The approach has been quite successful in deriving new information from expression data, and a number of methods and tools have been developed intensively in recent years. We review those methods and currently available tools, classify them according to the statistical methods employed, and discuss their pros and cons. We also discuss several interesting extensions to the methods.
Similar articles
-
Normalization and quantification of differential expression in gene expression microarrays.Brief Bioinform. 2006 Jun;7(2):166-77. doi: 10.1093/bib/bbl002. Epub 2006 Mar 7. Brief Bioinform. 2006. PMID: 16772260 Review.
-
Pre-processing of microarray data and analysis of differential expression.Methods Mol Biol. 2008;452:89-110. doi: 10.1007/978-1-60327-159-2_4. Methods Mol Biol. 2008. PMID: 18563370 Review.
-
Extensions to gene set enrichment.Bioinformatics. 2007 Feb 1;23(3):306-13. doi: 10.1093/bioinformatics/btl599. Epub 2006 Nov 24. Bioinformatics. 2007. PMID: 17127676
-
GEPS: the Gene Expression Pattern Scanner.Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W492-7. doi: 10.1093/nar/gkl067. Nucleic Acids Res. 2006. PMID: 16845057 Free PMC article.
-
Integration of statistical inference methods and a novel control measure to improve sensitivity and specificity of data analysis in expression profiling studies.J Biomed Inform. 2007 Oct;40(5):552-60. doi: 10.1016/j.jbi.2007.01.002. Epub 2007 Jan 19. J Biomed Inform. 2007. PMID: 17317331
Cited by
-
graphite - a Bioconductor package to convert pathway topology to gene network.BMC Bioinformatics. 2012 Jan 31;13:20. doi: 10.1186/1471-2105-13-20. BMC Bioinformatics. 2012. PMID: 22292714 Free PMC article.
-
Navigating Transcriptomic Connectivity Mapping Workflows to Link Chemicals with Bioactivities.Chem Res Toxicol. 2022 Nov 21;35(11):1929-1949. doi: 10.1021/acs.chemrestox.2c00245. Epub 2022 Oct 27. Chem Res Toxicol. 2022. PMID: 36301716 Free PMC article. Review.
-
Systems-level differential gene expression analysis reveals new genetic variants of oral cancer.Sci Rep. 2020 Sep 4;10(1):14667. doi: 10.1038/s41598-020-71346-7. Sci Rep. 2020. PMID: 32887903 Free PMC article.
-
Integrative pathway and network analysis provide insights on flooding-tolerance genes in soybean.Sci Rep. 2023 Feb 3;13(1):1980. doi: 10.1038/s41598-023-28593-1. Sci Rep. 2023. PMID: 36737640 Free PMC article.
-
ADGO 2.0: interpreting microarray data and list of genes using composite annotations.Nucleic Acids Res. 2011 Jul;39(Web Server issue):W302-6. doi: 10.1093/nar/gkr392. Epub 2011 May 29. Nucleic Acids Res. 2011. PMID: 21624890 Free PMC article.
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
Other Literature Sources
Miscellaneous
