GEOGLE: Context mining tool for the correlation between gene expression and the phenotypic distinction

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages 264-

  Yu, Yao ^a,b   Tu, Kang ^a   Zheng, Siyuan ^a   Li, Yun ^a   Ding, Guohui ^a   Ping, Jie ^d   Hao, Pei ^a,c   Li, Yixue ^a,b,c,d,e  

^a Chinese Academy of Sciences   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

^d SHANGHAI JIAO TONG UNIVERSITY   (China)

^e TONGJI UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMEDICAL ONTOLOGIES; BIOMEDICAL VOCABULARIES; GENE EXPRESSION ANALYSIS; GENE EXPRESSION DATASETS; GENE EXPRESSION DETECTION; MEDICAL SUBJECT HEADINGS; SCIENTIFIC RESEARCHES; SIGNALING PATHWAYS;

DATA PROCESSING; EXPERIMENTS; TOOLS;

GENE EXPRESSION;

ARTICLE; CIGARETTE SMOKING; DATA MINING; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENETIC ASSOCIATION; GENETIC DATABASE; GENOMICS; INFORMATION PROCESSING; INFORMATION RETRIEVAL; INFORMATION SERVICE; MEDICAL INFORMATION SYSTEM; ONLINE SYSTEM; PHENOTYPE; QUANTITATIVE ANALYSIS;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION; PHENOTYPE; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 70349757002     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-264     Document Type: Article

References (29)

1. Glinsky G.V, Berezovska O, Glinskii A.B. Microarray analysis identifies a death-from-cancer signature predicting therapy failure in patients with multiple types of cancer. J Clin Invest 2005, 115(6):1503-1521. 10.1172/JCI23412, 1136989, 15931389.
2. Vijver M.J, He Y.D, van't Veer L.J, Dai H, Hart A.A, Voskuil D.W, Schreiber G.J, Peterse J.L, Roberts C, Marton M.J. A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 2002, 347(25):1999-2009. 10.1056/NEJMoa021967, 12490681.
3. Hokamp K, Roche F.M, Acab M, Rousseau M.E, Kuo B, Goode D, Aeschliman D, Bryan J, Babiuk L.A, Hancock R.E. ArrayPipe: a flexible processing pipeline for microarray data. Nucleic Acids Res 2004, (32 Web Server):W457-459. 10.1093/nar/gkh446, 441584, 15215429.
4. Tarraga J, Medina I, Carbonell J, Huerta-Cepas J, Minguez P, Alloza E, Al-Shahrour F, Vegas-Azcarate S, Goetz S, Escobar P. GEPAS, a web-based tool for microarray data analysis and interpretation. Nucleic Acids Res 2008, (36 Web Server):W308-314. 10.1093/nar/gkn303, 2447723, 18508806.
5. Keller A, Backes C, Al-Awadhi M, Gerasch A, Kuntzer J, Kohlbacher O, Kaufmann M, Lenhof H.P. GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments. BMC Bioinformatics 2008, 9:552. 10.1186/1471-2105-9-552, 2627893, 19099609.
6. Morris J.A, Gayther S.A, Jacobs I.J, Jones C. A suite of Perl modules for handling microarray data. Bioinformatics 2008, 24(8):1102-1103. 10.1093/bioinformatics/btn085, 18353790.
7. Al-Shahrour F, Carbonell J, Minguez P, Goetz S, Conesa A, Tarraga J, Medina I, Alloza E, Montaner D, Dopazo J. Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments. Nucleic Acids Res 2008, (36 Web Server):W341-346. 10.1093/nar/gkn318, 2447758, 18515841.
8. Zhang B, Kirov S, Snoddy J. WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res 2005, (33 Web Server):W741-748. 10.1093/nar/gki475, 1160236, 15980575.
9. Rhodes D.R, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan A.M. Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci USA 2004, 101(25):9309-9314. 10.1073/pnas.0401994101, 438973, 15184677.
10. Rhodes D.R, Barrette T.R, Rubin M.A, Ghosh D, Chinnaiyan A.M. Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Res 2002, 62(15):4427-4433.
11. Hao P, Zheng S, Ping J, Tu K, Gieger C, Wang-Sattler R, Zhong Y, Li Y. Human gene expression sensitivity according to large scale meta-analysis. BMC Bioinformatics 2009, 10(Suppl 1):S56. 10.1186/1471-2105-10-S1-S56, 2648786, 19208159.
12. Lamb J. The Connectivity Map: a new tool for biomedical research. Nat Rev Cancer 2007, 7(1):54-60. 10.1038/nrc2044, 17186018.
13. Edgar R, Domrachev M, Lash A.E. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002, 30(1):207-210. 10.1093/nar/30.1.207, 99122, 11752295.
14. Barrett T, Edgar R. Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. Methods Enzymol 2006, 411:352-369. 10.1016/S0076-6879(06)11019-8, 1619900, 16939800.
15. Barrett T, Edgar R. Mining microarray data at NCBI's Gene Expression Omnibus (GEO). Methods Mol Biol 2006, 338:175-190. 1619899, 16888359.
16. Boyle J. Gene-Expression Omnibus integration and clustering tools in SeqExpress. Bioinformatics 2005, 21(10):2550-2551. 10.1093/bioinformatics/bti355, 15746290.
17. Sean D, Meltzer P.S. GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. Bioinformatics 2007, 23(14):1846-1847. 10.1093/bioinformatics/btm254, 17496320.
18. Yi Y, Li C, Miller C, George A.L. Strategy for encoding and comparison of gene expression signatures. Genome Biol 2007, 8(7):R133. 10.1186/gb-2007-8-7-r133, 2323223, 17612401.
19. Lowe H.J, Barnett G.O. Understanding and using the medical subject headings (MeSH) vocabulary to perform literature searches. JAMA 1994, 271(14):1103-1108. 10.1001/jama.271.14.1103, 8151853.
20. Tian L, Greenberg S.A, Kong S.W, Altschuler J, Kohane I.S, Park P.J. Discovering statistically significant pathways in expression profiling studies. Proc Natl Acad Sci USA 2005, 102(38):13544-13549. 10.1073/pnas.0506577102, 1200092,1200092, 16174746.
21. Sellers T.A, Huang Y, Cunningham J, Goode E.L, Sutphen R, Vierkant R.A, Kelemen L.E, Fredericksen Z.S, Liebow M, Pankratz V.S. Association of single nucleotide polymorphisms in glycosylation genes with risk of epithelial ovarian cancer. Cancer Epidemiol Biomarkers Prev 2008, 17(2):397-404. 10.1158/1055-9965.EPI-07-0565, 18268124.
22. Wright J.M, Merlo C.A, Reynolds J.B, Zeitlin P.L, Garcia J.G, Guggino W.B, Boyle M.P. Respiratory epithelial gene expression in patients with mild and severe cystic fibrosis lung disease. Am J Respir Cell Mol Biol 2006, 35(3):327-336. 10.1165/rcmb.2005-0359OC, 2643286, 16614352.
23. Wang-Sattler R, Yu Y, Mittelstrass K, Lattka E, Altmaier E, Gieger C, Ladwig K.H, Dahmen N, Weinberger K.M, Hao P. Metabolic profiling reveals distinct variations linked to nicotine consumption in humans-first results from the KORA study. PLoS One 2008, 3(12):e3863. 10.1371/journal.pone.0003863, 2588343, 19057651.
24. Rhodes D.R, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan A.M. ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia 2004, 6(1):1-6. 1635162, 15068665.
25. Rhodes D.R, Kalyana-Sundaram S, Mahavisno V, Varambally R, Yu J, Briggs B.B, Barrette T.R, Anstet M.J, Kincead-Beal C, Kulkarni P. Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia 2007, 9(2):166-180. 10.1593/neo.07112, 1813932, 17356713.
26. Praz V, Bucher P. CleanEx: new data extraction and merging tools based on MeSH term annotation. Nucleic Acids Res 2009, (37 Database):D880-884. 10.1093/nar/gkn878, 2686468, 19073704.
27. Rocca-Serra P, Brazma A, Parkinson H, Sarkans U, Shojatalab M, Contrino S, Vilo J, Abeygunawardena N, Mukherjee G, Holloway E. ArrayExpress: a public database of gene expression data at EBI. C R Biol 2003, 326(10-11):1075-1078. 10.1016/j.crvi.2003.09.026, 14744115.
28. Demeter J, Beauheim C, Gollub J, Hernandez-Boussard T, Jin H, Maier D, Matese J.C, Nitzberg M, Wymore F, Zachariah Z.K. The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Res 2007, (35 Database):D766-770. 10.1093/nar/gkl1019, 1781111, 17182626.
29. Zheng S, Sheng J, Wang C, Wang X, Yu Y, Li Y, Michie A, Dai J, Zhong Y, Hao P. MPSQ: a web tool for protein-state searching. Bioinformatics 2008, 24(20):2412-2413. 10.1093/bioinformatics/btn427, 18697766.