Functional classification analysis of somatically mutated genes in human breast and colorectal cancers

Genomics

Volumn 91, Issue 6, 2008, Pages 508-511

  Chittenden, Thomas W ^a,b,c   Howe, Eleanor A ^a   Culhane, Aedin C ^a,b   Sultana, Razvan ^a   Taylor, Jennifer M ^d   Holmes, Chris ^c,e   Quackenbush, John ^a,b  

^a DANA FARBER CANCER INSTITUTE   (United States)

^b HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d UNIVERSITY OF OXFORD   (United Kingdom)

^e MRC MAMMALIAN GENETICS UNIT   (United Kingdom)

Author keywords

Bioinformatics; Breast cancer; Colorectal cancer; Genomics

Indexed keywords

GUANOSINE TRIPHOSPHATASE; SMAD PROTEIN; STRESS ACTIVATED PROTEIN KINASE; TRANSFORMING GROWTH FACTOR BETA1;

ARTICLE; BREAST CANCER; COLORECTAL CANCER; GENE IDENTIFICATION; GENE MUTATION; GENE SEQUENCE; GENETIC ANALYSIS; HUMAN; PRIORITY JOURNAL; PROTEIN INTERACTION;

BREAST NEOPLASMS; COLORECTAL NEOPLASMS; COMPUTATIONAL BIOLOGY; DNA MUTATIONAL ANALYSIS; GENE EXPRESSION REGULATION, NEOPLASTIC; GENES, NEOPLASM; HUMANS; MUTATION; SOFTWARE; TRANSFORMING GROWTH FACTOR BETA1;

EID: 44649115241     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2008.03.002     Document Type: Article

References (21)

1. Sjoblom T., Jones S., Wood L.D., Parsons D.W., Lin J., Barber T.D., Mandelker D., Leary R.J., Ptak J., Silliman N., Szabo S., Buckhaults P., Farrell C., Meeh P., Markowitz S.D., Willis J., Dawson D., Willson J.K., Gazdar A.F., Hartigan J., Wu L., Liu C., Parmigiani G., Park B.H., Bachman K.E., Papadopoulos N., Vogelstein B., Kinzler K.W., and Velculescu V.E. The consensus coding sequences of human breast and colorectal cancers. Science 314 (2006) 268-274
2. Vogelstein B., and Kinzler K.W. Cancer genes and the pathways they control. Nat. Med. 10 (2004) 789-799
3. C. Database, URL: http://www.ncbi.nlm.nih.gov/CCDS.
4. Hosack D.A., Dennis Jr. G., Sherman B.T., Lane H.C., and Lempicki R.A. Identifying biological themes within lists of genes with EASE. Genome Biol. 4 (2003) R70
5. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., Harris M.A., Hill D.P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J.C., Richardson J.E., Ringwald M., Rubin G.M., and Sherlock G. Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25 (2000) 25-29
6. Pfam, URL: http://www.sanger.ac.uk/Software/Pfam/.
7. Boeckmann B., Bairoch A., Apweiler R., Blatter M.C., Estreicher A., Gasteiger E., Martin M.J., Michoud K., O C., 'Donovan, Phan I., Pilbout S., and Schneider M. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31 (2003) 365-370
8. Becker K.G., White S.L., Muller J., and Engel J. BBID: the biological biochemical image database. Bioinformatics 16 (2000) 745-746
9. Dahlquist K.D., Salomonis N., Vranizan K., Lawlor S.C., and Conklin B.R. GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat. Genet. 31 (2002) 19-20
10. Ogata H., Goto S., Sato K., Fujibuchi W., Bono H., and Kanehisa M. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 27 (1999) 29-34
11. Chen H., and Sharp B.M. Content-rich biological network constructed by mining PubMed abstracts. BMC Bioinformatics 5 (2004) 147
12. Biswas S., Chytil A., Washington K., Romero-Gallo J., Gorska A.E., Wirth P.S., Gautam S., Moses H.L., and Grady W.M. Transforming growth factor beta receptor type II inactivation promotes the establishment and progression of colon cancer. Cancer Res. 64 (2004) 4687-4692
13. Ogino S., Kawasaki T., Ogawa A., Kirkner G.J., Loda M., and Fuchs C.S. TGFBR2 mutation is correlated with CpG island methylator phenotype in microsatellite instability-high colorectal cancer. Hum. Pathol. 38 (2007) 614-620
14. Wang B., Kishihara K., Zhang D., Sakamoto T., and Nomoto K. Transcriptional regulation of a receptor protein tyrosine phosphatase gene hPTP-J by PKC-mediated signaling pathways in Jurkat and Molt-4 T lymphoma cells. Biochim. Biophys. Acta 1450 (1999) 331-340
15. Yan H.X., Yang W., Zhang R., Chen L., Tang L., Zhai B., Liu S.Q., Cao H.F., Man X.B., Wu H.P., Wu M.C., and Wang H.Y. Protein-tyrosine phosphatase PCP-2 inhibits beta-catenin signaling and increases E-cadherin-dependent cell adhesion. J. Biol. Chem. 281 (2006) 15423-15433
16. Heidenreich O., Krauter J., Riehle H., Hadwiger P., John M., Heil G., Vornlocher H.P., and Nordheim A. AML1/MTG8 oncogene suppression by small interfering RNAs supports myeloid differentiation of t(8;21)-positive leukemic cells. Blood 101 (2003) 3157-3163
17. Herbst A., and Kolligs F.T. Wnt signaling as a therapeutic target for cancer. Methods Mol. Biol. 361 (2007) 63-91
18. Perou C.M., Jeffrey S.S., van de Rijn M., Rees C.A., Eisen M.B., Ross D.T., Pergamenschikov A., Williams C.F., Zhu S.X., Lee J.C., Lashkari D., Shalon D., Brown P.O., and Botstein D. Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc. Natl. Acad. Sci. U. S. A. 96 (1999) 9212-9217
19. Calonge M.J., Seoane J., and Massague J. Opposite Smad and chicken ovalbumin upstream promoter transcription factor inputs in the regulation of the collagen VII gene promoter by transforming growth factor-beta. J. Biol. Chem. 279 (2004) 23759-23765
20. Brown T.L., Patil S., Cianci C.D., Morrow J.S., and Howe P.H. Transforming growth factor beta induces caspase 3-independent cleavage of alphaII-spectrin (alpha-fodrin) coincident with apoptosis. J. Biol. Chem. 274 (1999) 23256-23262
21. Saeed A.I., Bhagabati N.K., Braisted J.C., Liang W., Sharov V., Howe E.A., Li J., Thiagarajan M., White J.A., and Quackenbush J. TM4 microarray software suite. Methods Enzymol. 411 (2006) 134-193