EnrichNet: Network-based gene set enrichment analysis

Bioinformatics

Volumn 28, Issue 18, 2012, Pages

  Glaab, Enrico ^a   Baudot, Anaïs ^b   Krasnogor, Natalio ^c   Schneider, Reinhard ^a   Valencia, Alfonso ^d  

^a UNIVERSITY OF LUXEMBOURG   (Luxembourg)

^b AIX MARSEILLE UNIVERSITÉ   (France)

^c UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^d Centro Nacional de Investigaciones Oncológicas   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; GENE; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; GENETIC DATABASE; GENETICS; HUMAN; INTERNET; METABOLISM; METHODOLOGY; NEOPLASM; PARKINSON DISEASE; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; STATISTICAL ANALYSIS;

DATA INTERPRETATION, STATISTICAL; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; GENES; HUMANS; INTERNET; NEOPLASMS; PARKINSON DISEASE; PROTEIN INTERACTION MAPPING; PROTEIN INTERACTION MAPS; SOFTWARE;

EID: 84866449583     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts389     Document Type: Article

References (48)

1. Al-Shahrour et al. (2007) From genes to functional classes in the study of biological systems. BMC Bioinformatics, 8, 114.
2. Alon,U. et al. (1999) Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl. Acad. Sci. USA, 96, 6745.
3. Apweiler,R. et al. (2001) The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res., 29, 37.
4. Ashburner,M. et al. (2000) Gene Ontology: tool for the unification of biology. Nat. Genet., 25, 25-29.
5. Backes,C. et al. (2007) GeneTrail-advanced gene set enrichment analysis. Nucleic Acids Res., 35 (Suppl. 2), W186.
6. Bamford,S. et al. (2004) The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. Br. J. Cancer, 91, 355-358.
7. Bauer,S. et al. (2008) Ontologizer 2.0-a multifunctional tool for GO term enrichment analysis and data exploration. Bioinformatics, 24, 1650.
8. Beer,D. et al. (2002) Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat. Med., 8, 816-824.
9. Benjamini,Y. & Hochberg,Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Statist. Soc. Ser. B, 57, 289-300.
10. Bhattacharjee,A. et al. (2001) Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc. Natl. Acad. Sci. USA, 98, 13790.
11. Blum-Degena,D. et al. (1995) Interleukin-1 [beta] and interleukin-6 are elevated in the cerebrospinal fluid of Alzheimer's and de novo Parkinson's disease patients. Neurosci. Lett., 202, 17-20.
12. Breslin,T. et al. (2004) Comparing functional annotation analyses with Catmap. BMC Bioinformatics, 5, 193.
13. Carmona-Saez,P. et al. (2007) GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists. Genome Biol., 8, R3.
14. del Pulgar,T. et al. (2005) Rho GTPase expression in tumourigenesis: evidence for a significant link. Bioessays, 27, 602-613.
15. Dennis Jr,G. et al. (2003) DAVID: database for annotation, visualization, and integrated discovery. Genome Biol., 4, P3.
16. Dinu,I. et al. (2007) Improving gene set analysis of microarray data by SAM-GS. BMC Bioinformatics, 8, 242.
17. Fujiwara,Y. et al. (2012) Fast and exact top-k search for random walk with restart. Proc. VLDB Endowment, 5, 442-453.
18. Futreal,P. et al. (2004) A census of human cancer genes. Nat. Rev. Cancer, 4, 177-183.
19. Glaab,E. et al. (2010a) Extending pathways and processes using molecular interaction networks to analyse cancer genome data. BMC Bioinformatics, 11, 597.
20. Glaab,E. et al. (2010b) TopoGSA: network topological gene set analysis. Bioinformatics, 26, 1271-1272.
21. Hamosh,A. et al. (2000) Online Mendelian inheritance in man (OMIM). Hum. Mutat., 15, 57-61.
22. Huang,D. et al. (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res., 37, 1-13.
23. Huber,W. et al. (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics, 18 (Suppl. 1), S96-S104.
24. Hung,J. et al. (2012) Gene set enrichment analysis: performance evaluation and usage guidelines. Brief. Bioinform., 13, 281-291.
25. Joshi-Tope,G. et al. (2005) Reactome: a knowledgebase of biological pathways. Nucleic Acids Res., 33 (Suppl. 1), D428.
26. Kanehisa,M. et al. (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res., 34 (Database Issue), D354-D357.
27. Kang,W. et al. (2005) Induction of DMBT1 expression by reduced ERK activity during a gastric mucosa differentiation-like process and its association with human gastric cancer. Carcinogenesis, 26, 1129.
28. Kim,S. and Volsky,D. (2005) PAGE: parametric analysis of gene set enrichment. BMC Bioinformatics, 6, 144.
29. Knott,C. et al. (2000) Inflammatory regulators in Parkinson's disease: iNOS, lipocortin-1, and cyclooxygenases-1 and-2. Mol. Cell. Neurosci., 16, 724-739.
30. Köhler,S. et al. (2008) Walking the interactome for prioritization of candidate disease genes. Am. J. Human Genet., 82, 949-958.
31. Lee,H. et al. (2005) ErmineJ: tool for functional analysis of gene expression data sets. BMC Bioinformatics, 6, 269.
32. Luo,W. et al. (2009) GAGE: generally applicable gene set enrichment for pathway analysis. BMC Bioinformatics, 10, 161.
33. Mootha,V. et al. (2003) PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet., 34, 267-273.
34. Nishimura,D. (2001) BioCarta. Biotech Software & Internet Report, 2, 117-120.
35. Olmea,O. et al. (1999) Effective use of sequence correlation and conservation in fold recognition. J. Mol. Biol., 293, 1221-1239.
36. Pico,A. et al. (2008) WikiPathways: pathway editing for the people. PLoS Biol., 6, e184.
37. Schaefer,C. et al. (2009) PID: the pathway interaction database. Nucleic Acids Res., 37 (Suppl. 1), D674.
38. Shin,J. et al. (2007) Lesional gene expression profiling in cutaneous t-cell lymphoma reveals natural clusters associated with disease outcome. Blood, 110, 3015-3027.
39. Smyth,G. (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol., 3, 3.
40. Snel,B. et al. (2000) STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res., 28, 3442-3444.
41. Subramanian,A. et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA, 102, 15545.
42. Tong,H. et al. (2008) Random walk, with restart: fast solutions and applications. Knowledge Information Syst., 14, 327-346.
43. Tu,K. et al. (2005) MEGO: gene functional module expression based on gene ontology. Biotechniques, 38, 277-283.
44. Von Mering,C. et al. (2003) STRING: a database of predicted functional associations between proteins. Nucleic Acids Res., 31, 258-261.
45. Wolpert,D. & Macready,W. (1995) No free lunch theorems for search. Technical report SFI-TR-95-02-010, Santa Fe, NM.
46. Wu,F. et al. (2008) RNA-interference-mediated Cdc42 silencing down-regulates phosphorylation of STAT3 and suppresses growth in human bladder-cancer cells. Biotechnol. Appl. Biochem., 49, 121-128.
47. Yin,Z. et al. (2010) A unified framework for link recommendation using random walks. In Proceedings of the 2010 International Conference on Advances in Social Networks Analysis and Mining, IEEE Computer Society, Odense, Denmark, pp. 152-159.
48. Yu,W. et al. (2010) Phenopedia and genopedia: disease-centered and gene-centered views of the evolving knowledge of human genetic associations. Bioinformatics, 26, 145.