| [1] | Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM (1999) Systematic determination of genetic network architecture. Nat Genet 22(3): 281–285. doi: 10.1038/10343
|
| [2] | Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25(1): 25–29.
|
| [3] | Dahlquist KD, Salomonis N, Vranizan K, Lawlor SC, Conklin BR (2002) GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat Genet 31(1): 19–20. doi: 10.1038/ng0502-19
|
| [4] | Al-Shahrour F, Díaz-Uriarte R, Dopazo J (2004) FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics 20(4): 578–580. doi: 10.1093/bioinformatics/btg455
|
| [5] | Boyle EI, Weng S, Gollub J, Jin H, Botstein D, et al. (2004) TermFinder–open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 20(18): 3710–3715. doi: 10.1093/bioinformatics/bth456
|
| [6] | Chung HJ, Kim M, Park CH, Kim J, Kim JH (2004) ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics. Nucleic Acids Res 32(Web Server issue): W460–464. doi: 10.1093/nar/gkh476
|
| [7] | Zhang B, Schmoyer D, Kirov S, Snoddy J (2004) GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. BMC Bioinformatics 5: 16.
|
| [8] | Zhong S, Storch KF, Lipan O, Kao MC, Weitz CJ, et al. (2004) GoSurfer: a graphical interactive tool for comparative analysis of large gene sets in Gene Ontology space. Appl Bioinformatics 3(4): 261–264. doi: 10.2165/00822942-200403040-00009
|
| [9] | Chung HJ, Park CH, Han MR, Lee S, Ohn JH, et al. (2005) ArrayXPath II: mapping and visualizing microarray gene-expression data with biomedical ontologies and integrated biological pathway resources using Scalable Vector Graphics. Nucleic Acids Res 33(Web Server issue): W621–626. doi: 10.1093/nar/gki450
|
| [10] | Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, et al. (2003) PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 34(3): 267–273. doi: 10.1038/ng1180
|
| [11] | Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102(43): 15545–15550. doi: 10.1073/pnas.0506580102
|
| [12] | Cho SB, Kim J, Kim JH (2009) Identifying set-wise differential co-expression in gene expression microarray data. BMC Bioinformatics 10: 109. doi: 10.1186/1471-2105-10-109
|
| [13] | Kim J, Chung HJ, Jung Y, Kim KK, Kim JH (2008) BioLattice: a framework for the biological interpretation of microarray gene expression data using concept lattice analysis. J Biomed Inform 41(2): 232–241. doi: 10.1016/j.jbi.2007.10.003
|
| [14] | Yue L, Reisdorf WC (2005) Pathway and ontology analysis: emerging approaches connecting transcriptome data and clinical endpoints. Curr Mol Med 5(1): 11–21. doi: 10.2174/1566524053152906
|
| [15] | Caspi R, Altman T, Dale JM, Dreher K, Fulcher CA, et al. (2010) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 38(Database issue): D473–479. doi: 10.1093/nar/gkp875
|
| [16] | Alexa A, Rahnenführer J, Lengauer T (2006) Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22(13): 1600–1607. doi: 10.1093/bioinformatics/btl140
|
| [17] | Falcon S, Gentleman R (2007) Using GOstats to test gene lists for GO term association. Bioinformatics 23(2): 257–258. doi: 10.1093/bioinformatics/btl567
|
| [18] | Huang da W, Sherman BT, Lempicki RA (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37(1): 1–13. doi: 10.1093/nar/gkn923
|
| [19] | Goeman JJ, Buhlmann P (2007) Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics 23(8): 980–987. doi: 10.1093/bioinformatics/btm051
|
| [20] | Bild AH, Yao G, Chang JT, Wang Q, Potti A, et al. (2006) Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature 439(7074): 353–357. doi: 10.1038/nature04296
|
| [21] | Potti A, Dressman HK, Bild A, Riedel RF, Chan G (2006) Genomic signatures to guide the use of chemotherapeutics. Nat Med 12(11): 1294–1300. doi: 10.1038/nm1491
|
| [22] | Barry WT, Nobel AB, Wright FA (2005) Significance analysis of functional categories in gene expression studies: a structured permutation approach. Bioinformatics 21(9): 1943–1949. doi: 10.1093/bioinformatics/bti260
|
| [23] | Li KC (2002) Genome-wide co-expression dynamics: theory and application. Proc Natl Acad Sci U S A 99(26): 16875–16880. doi: 10.1073/pnas.252466999
|
| [24] | Lai Y, Wu B, Chen L, Zhao H (2004) A statistical method for identifying differential gene-gene co-expression patterns. Bioinformatics 20(17): 3146–55. doi: 10.1093/bioinformatics/bth379
|
| [25] | Choi JK, Yu U, Yoo OJ, Kim S (2005) Differential co-expression analysis using microarray data and its application to human cancer. Bioinformatics 21(24): 4348–4355. doi: 10.1093/bioinformatics/bti722
|
| [26] | Kostka D, Spang R (2004) Finding disease specific alterations in the co-expression of genes. Bioinformatics 20 Suppl 1: i194–199. doi: 10.1093/bioinformatics/bth909
|
| [27] | Watson M (2006) CoXpress: differential co-expression in gene expression data. BMC Bioinformatics 7: 509.
|
| [28] | Kim JH, Ha IS, Hwang CI, Lee YJ, Kim Y, et al. (2004) Gene expression profiling of anti-GBM glomerulonephritis model: the role of NFkB in immune complex-mediated kidney disease. Kidney International 66(5): 1826–1837. doi: 10.1111/j.1523-1755.2004.00956.x
|
| [29] | Ganter B, Wille R (1999) Formal concept analysis: mathematical foundations. Berlin; New York: Springer.
|
| [30] | Emmert-Streib F, Dehmer M (2010) Medical Biostatistics for Complex Diseases. Wiley doi: 10.1002/9783527630332
|
