Briefings in Bioinformatics Advance Access published online on January 17, 2008
Briefings in Bioinformatics, doi:10.1093/bib/bbn001
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Gene-set approach for expression pattern analysis
Corresponding author. Seon-Young Kim, Functional Genomics Research Center, KRIBB, 111 Gwahangno, Yuseong-gu, Daejeon 305-806, Korea. Tel: 82-42-879-8116; Fax: 82-42-879-8110; E-mail: kimsy{at}kribb.re.kr
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.
Keywords: gene set analysis, DNA microarray, differential expression of genes
Submitted: November 7, 2007. Received (in revised form): December 28, 2007.
![]()
CiteULike
Connotea
Del.icio.us What's this?
This article has been cited by other articles:
![]() |
A. Keller, C. Backes, A. Gerasch, M. Kaufmann, O. Kohlbacher, E. Meese, and H.-P. Lenhof A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis Bioinformatics, November 1, 2009; 25(21): 2787 - 2794. [Abstract] [Full Text] [PDF] |
||||
![]() |
D. Glez-Pena, G. Gomez-Lopez, D. G. Pisano, and F. Fdez-Riverola WhichGenes: a web-based tool for gathering, building, storing and exporting gene sets with application in gene set enrichment analysis Nucleic Acids Res., July 1, 2009; 37(suppl_2): W329 - W334. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Nam, M. Li, K. Choi, C. Balch, S. Kim, and K. P. Nephew MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression Nucleic Acids Res., July 1, 2009; 37(suppl_2): W356 - W362. [Abstract] [Full Text] [PDF] |
||||
![]() |
P. Du, G. Feng, J. Flatow, J. Song, M. Holko, W. A. Kibbe, and S. M. Lin From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations Bioinformatics, June 15, 2009; 25(12): i63 - i68. [Abstract] [Full Text] [PDF] |
||||
![]() |
R. Heller, E. Manduchi, G. R. Grant, and W. J. Ewens A flexible two-stage procedure for identifying gene sets that are differentially expressed Bioinformatics, April 15, 2009; 25(8): 1019 - 1025. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Ma and M. R. Kosorok Identification of differential gene pathways with principal component analysis Bioinformatics, April 1, 2009; 25(7): 882 - 889. [Abstract] [Full Text] [PDF] |
||||
![]() |
C.-A. Tsai and J. J. Chen Multivariate analysis of variance test for gene set analysis Bioinformatics, April 1, 2009; 25(7): 897 - 903. [Abstract] [Full Text] [PDF] |
||||
![]() |
I. Dinu, J. D. Potter, T. Mueller, Q. Liu, A. J. Adewale, G. S. Jhangri, G. Einecke, K. S. Famulski, P. Halloran, and Y. Yasui Gene-set analysis and reduction Brief Bioinform, January 1, 2009; 10(1): 24 - 34. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. Tarraga, I. Medina, J. Carbonell, J. Huerta-Cepas, P. Minguez, E. Alloza, F. Al-Shahrour, S. Vegas-Azcarate, S. Goetz, P. Escobar, et al. GEPAS, a web-based tool for microarray data analysis and interpretation Nucleic Acids Res., July 1, 2008; 36(suppl_2): W308 - W314. [Abstract] [Full Text] [PDF] |
||||


