Inferring pathways from gene lists using a literature-derived network of biological relationships

Bioinformatics

Volumn 21, Issue 6, 2005, Pages 788-793

  Rajagopalan, Dilip ^a   Agarwal, Pankaj ^a  

^a GLAXOSMITHKLINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANALYTIC METHOD; ARTICLE; COMPUTER SIMULATION; CONTROLLED STUDY; EXPERIMENTATION; GENE INTERACTION; GENE NUMBER; GENETIC DATABASE; INFORMATION PROCESSING; INTERMETHOD COMPARISON; MEDICAL LITERATURE; METABOLITE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SCORING SYSTEM; SENSITIVITY AND SPECIFICITY; SIGNAL TRANSDUCTION; VALIDATION PROCESS;

MAMMALIA;

EID: 15944402798     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti069     Document Type: Article

References (9)

1. Barabasi,A.-L. and Oltvai,Z.N. (2004) Network biology: understanding the cell's functional organization. Nat. Rev. Genet., 5, 101-114.
2. Dahlquist,K.D., Salomonis,N., Vranizan,K., Lawlor,S.C. and Conklin,B.R. (2002) Gen-MAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat. Genet., 31, 19-20.
3. Draghici,S., Khatri,P., Martins,R.P., Ostermeier,G.C. and Krawetz,S.A. (2003) Global functional profiling of gene expression. Genomics, 81, 98-104.
4. Hosack,D.A., Dennis,G.,Jr, Sherman,B.T., Lane,H.C. and Lempicki,R.A. (2003) Identifying biological themes within lists of genes with EASE. Genome Biol., 4, R70.
5. Ideker,T., Ozier,O., Schwikoswki,B. and Siegel,A.F. (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics, 18(Suppl. 1), S233-S240.
6. Jenssen,T.-K., Leagreid,A., Komorowski,J. and Hovig,E. (2001) A literature network of human genes for high-throughput analysis of gene expression. Nat. Genet., 28, 21-28.
7. Matys,V., Fricke,E., Geffers,R., Gossling,E., Haubrock,M., Hehl,R., Hornischer.K., Karas,D., Kel,A.E., Kel-Margoulis,O.V. et al. (2003) Transfac: transcriptional regulation, from patterns to profiles. Nucleic Acids Res., 31, 374-378.
8. Mootha,V., Lindgren,C., Eriksson,K., Subramanian,A., Sihag,S., Lehar,J., Puigserver,P., Carlsson,E., Ridderstrale,M., Laurila,E. et al. (2003) PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet., 34, 267-273.
9. Tavazoie,S., Hughes,J.D., Campbell,M.J., Cho,R.J. and Church,G.M. (1999) Systematic determination of genetic network architechture. Nat. Genet., 22(3), 281-285.