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PMID: 17693572 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

A multidimensional analysis of genes mutated in breast and colorectal cancers.

Genome research ·Vol. 17 ·No. 9 ·2007-09-00 ·Pages 1304-18

Lin J, Gan CM, Zhang X, Jones S, Sjöblom T, Wood LD, Parsons DW, Papadopoulos N, Kinzler KW, Vogelstein B, Parmigiani G, Velculescu VE

Abstract

A recent study of a large number of genes in a panel of breast and colorectal cancers identified somatic mutations in 1149 genes. To identify potential biological processes affected by these genes, we examined their putative roles based on sequence similarity, membership in known functional groups and pathways, and predicted interactions with other proteins. These analyses identified functional groups and pathways that were enriched for mutated genes in both tumor types. Additionally, the results pointed to differences in molecular mechanisms that underlie breast and colorectal cancers, including various intracellular signaling and metabolic pathways. These studies provide a multidimensional framework to guide further research and help identify cellular processes critical for malignant progression and therapeutic intervention.

MeSH Terms
Amino Acid Sequence Breast Neoplasms/classification,genetics,metabolism Cluster Analysis Colorectal Neoplasms/classification,genetics,metabolism Female Gene Expression Regulation, Neoplastic Genes, Neoplasm Humans Models, Biological Molecular Sequence Data Mutation Neoplasm Proteins/chemistry,genetics,metabolism Protein Structure, Tertiary Sequence Homology, Amino Acid
Chemicals
Neoplasm Proteins
Authors & Affiliations
12 authors, click to expand affiliations / ORCID
Lin Jimmy
Ludwig Center for Cancer Genetics and Therapeutics, and The Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland 21231, USA.
Gan Christine M
Zhang Xiaosong
Jones Siân
Sjöblom Tobias
Wood Laura D
Parsons D Williams
Papadopoulos Nickolas
Kinzler Kenneth W
Vogelstein Bert
Parmigiani Giovanni
Velculescu Victor E
References (25)
25 references, click to expand
  1. Mediators of vascular remodelling co-opted for sequential steps in lung metastasis.
    Nature. 2007 Apr 12;446(7137):765-70 PMID: 17429393
  2. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
    Nat Genet. 2000 May;25(1):25-9 PMID: 10802651
  3. The circadian gene Period2 plays an important role in tumor suppression and DNA damage response in vivo.
    Cell. 2002 Oct 4;111(1):41-50 PMID: 12372299
  4. Osprey: a network visualization system.
    Genome Biol. 2003;4(3):R22 PMID: 12620107
  5. A protein interaction map of Drosophila melanogaster.
    Science. 2003 Dec 5;302(5651):1727-36 PMID: 14605208
  6. Nuclear transport and cancer: from mechanism to intervention.
    Nat Rev Cancer. 2004 Feb;4(2):106-17 PMID: 14732865
  7. A map of the interactome network of the metazoan C. elegans.
    Science. 2004 Jan 23;303(5657):540-3 PMID: 14704431
  8. The Gene Ontology Annotation (GOA) Database--an integrated resource of GO annotations to the UniProt Knowledgebase.
    In Silico Biol. 2004;4(1):5-6 PMID: 15089749
  9. Cancer genes and the pathways they control.
    Nat Med. 2004 Aug;10(8):789-99 PMID: 15286780
  10. Basic local alignment search tool.
    J Mol Biol. 1990 Oct 5;215(3):403-10 PMID: 2231712
  11. KEGG: Kyoto Encyclopedia of Genes and Genomes.
    Nucleic Acids Res. 1999 Jan 1;27(1):29-34 PMID: 9847135
  12. GOToolBox: functional analysis of gene datasets based on Gene Ontology.
    Genome Biol. 2004;5(12):R101 PMID: 15575967
  13. Deregulated expression of the PER1, PER2 and PER3 genes in breast cancers.
    Carcinogenesis. 2005 Jul;26(7):1241-6 PMID: 15790588
  14. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae.
    Nature. 2000 Feb 10;403(6770):623-7 PMID: 10688190
  15. Tumor suppression by the mammalian Period genes.
    Cancer Causes Control. 2006 May;17(4):525-30 PMID: 16596306
  16. The InterPro database, an integrated documentation resource for protein families, domains and functional sites.
    Nucleic Acids Res. 2001 Jan 1;29(1):37-40 PMID: 11125043
  17. Distinct oligomeric states of SMAD proteins in the transforming growth factor-beta pathway.
    J Biol Chem. 2000 Dec 29;275(52):40710-7 PMID: 11018029
  18. A comprehensive two-hybrid analysis to explore the yeast protein interactome.
    Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4569-74 PMID: 11283351
  19. Matrix metalloproteinases and tumor metastasis.
    Cancer Metastasis Rev. 2006 Mar;25(1):9-34 PMID: 16680569
  20. Global topological features of cancer proteins in the human interactome.
    Bioinformatics. 2006 Sep 15;22(18):2291-7 PMID: 16844706
  21. The consensus coding sequences of human breast and colorectal cancers.
    Science. 2006 Oct 13;314(5797):268-74 PMID: 16959974
  22. NUP98 fusion in human leukemia: dysregulation of the nuclear pore and homeodomain proteins.
    Int J Hematol. 2005 Jul;82(1):21-7 PMID: 16105755
  23. Discovering statistically significant pathways in expression profiling studies.
    Proc Natl Acad Sci U S A. 2005 Sep 20;102(38):13544-9 PMID: 16174746
  24. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
    Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50 PMID: 16199517
  25. Targeting polyamine metabolism and function in cancer and other hyperproliferative diseases.
    Nat Rev Drug Discov. 2007 May;6(5):373-90 PMID: 17464296
Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.6431107
Published
2007-09-00
Epub
2007-00-10
Pages
1304-18
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC1950899
Subset
IM
Grants
NCI NIH HHS · CA 57345 · United States
NCI NIH HHS · R37 CA043460 · United States
PHS HHS · HHSN261200433002C · United States
NCI NIH HHS · P50 CA062924 · United States
NCI NIH HHS · CA62924 · United States
NCI NIH HHS · CA 121113 · United States
NCI NIH HHS · R01 CA121113 · United States
NCI NIH HHS · CA 43460 · United States
NCI NIH HHS · R37 CA057345 · United States
NCI NIH HHS · R01 CA057345 · United States
NCI NIH HHS · R01 CA105090 · United States
NCI NIH HHS · CA105090-03 · United States
External Links
PubMed source DOI: 10.1101/gr.6431107 PMC Full Text View journal details
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