Literature DB >> 17693572

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

Jimmy Lin1, Christine M Gan, Xiaosong Zhang, Siân Jones, Tobias Sjöblom, Laura D Wood, D Williams Parsons, Nickolas Papadopoulos, Kenneth W Kinzler, Bert Vogelstein, Giovanni Parmigiani, Victor E Velculescu.   

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.

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Year:  2007        PMID: 17693572      PMCID: PMC1950899          DOI: 10.1101/gr.6431107

Source DB:  PubMed          Journal:  Genome Res        ISSN: 1088-9051            Impact factor:   9.043


  25 in total

1.  Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors:  M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal:  Nat Genet       Date:  2000-05       Impact factor: 38.330

Review 2.  Nuclear transport and cancer: from mechanism to intervention.

Authors:  Tweeny R Kau; Jeffrey C Way; Pamela A Silver
Journal:  Nat Rev Cancer       Date:  2004-02       Impact factor: 60.716

3.  The Gene Ontology Annotation (GOA) Database--an integrated resource of GO annotations to the UniProt Knowledgebase.

Authors:  Evelyn Camon; Daniel Barrell; Vivian Lee; Emily Dimmer; Rolf Apweiler
Journal:  In Silico Biol       Date:  2003-12-01

4.  Basic local alignment search tool.

Authors:  S F Altschul; W Gish; W Miller; E W Myers; D J Lipman
Journal:  J Mol Biol       Date:  1990-10-05       Impact factor: 5.469

5.  The circadian gene Period2 plays an important role in tumor suppression and DNA damage response in vivo.

Authors:  Loning Fu; Helene Pelicano; Jinsong Liu; Peng Huang; Cheng Lee
Journal:  Cell       Date:  2002-10-04       Impact factor: 41.582

Review 6.  Cancer genes and the pathways they control.

Authors:  Bert Vogelstein; Kenneth W Kinzler
Journal:  Nat Med       Date:  2004-08       Impact factor: 53.440

7.  A protein interaction map of Drosophila melanogaster.

Authors:  L Giot; J S Bader; C Brouwer; A Chaudhuri; B Kuang; Y Li; Y L Hao; C E Ooi; B Godwin; E Vitols; G Vijayadamodar; P Pochart; H Machineni; M Welsh; Y Kong; B Zerhusen; R Malcolm; Z Varrone; A Collis; M Minto; S Burgess; L McDaniel; E Stimpson; F Spriggs; J Williams; K Neurath; N Ioime; M Agee; E Voss; K Furtak; R Renzulli; N Aanensen; S Carrolla; E Bickelhaupt; Y Lazovatsky; A DaSilva; J Zhong; C A Stanyon; R L Finley; K P White; M Braverman; T Jarvie; S Gold; M Leach; J Knight; R A Shimkets; M P McKenna; J Chant; J M Rothberg
Journal:  Science       Date:  2003-11-06       Impact factor: 47.728

8.  A map of the interactome network of the metazoan C. elegans.

Authors:  Siming Li; Christopher M Armstrong; Nicolas Bertin; Hui Ge; Stuart Milstein; Mike Boxem; Pierre-Olivier Vidalain; Jing-Dong J Han; Alban Chesneau; Tong Hao; Debra S Goldberg; Ning Li; Monica Martinez; Jean-François Rual; Philippe Lamesch; Lai Xu; Muneesh Tewari; Sharyl L Wong; Lan V Zhang; Gabriel F Berriz; Laurent Jacotot; Philippe Vaglio; Jérôme Reboul; Tomoko Hirozane-Kishikawa; Qianru Li; Harrison W Gabel; Ahmed Elewa; Bridget Baumgartner; Debra J Rose; Haiyuan Yu; Stephanie Bosak; Reynaldo Sequerra; Andrew Fraser; Susan E Mango; William M Saxton; Susan Strome; Sander Van Den Heuvel; Fabio Piano; Jean Vandenhaute; Claude Sardet; Mark Gerstein; Lynn Doucette-Stamm; Kristin C Gunsalus; J Wade Harper; Michael E Cusick; Frederick P Roth; David E Hill; Marc Vidal
Journal:  Science       Date:  2004-01-02       Impact factor: 47.728

9.  Mediators of vascular remodelling co-opted for sequential steps in lung metastasis.

Authors:  Gaorav P Gupta; Don X Nguyen; Anne C Chiang; Paula D Bos; Juliet Y Kim; Cristina Nadal; Roger R Gomis; Katia Manova-Todorova; Joan Massagué
Journal:  Nature       Date:  2007-04-12       Impact factor: 49.962

10.  Osprey: a network visualization system.

Authors:  Bobby-Joe Breitkreutz; Chris Stark; Mike Tyers
Journal:  Genome Biol       Date:  2003-02-27       Impact factor: 13.583

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  63 in total

1.  Expression of the novel human gene, UBE2Q1, in breast tumors.

Authors:  Atefeh Seghatoleslam; Mohsen Nikseresht; Sayed Mohammad Shafiee; Ahmad Monabati; Mohammad Mehdi Namavari; Abdolrassul Talei; Akbar Safaei; Ali Akbar Owji
Journal:  Mol Biol Rep       Date:  2011-12-14       Impact factor: 2.316

2.  PathScan: a tool for discerning mutational significance in groups of putative cancer genes.

Authors:  Michael C Wendl; John W Wallis; Ling Lin; Cyriac Kandoth; Elaine R Mardis; Richard K Wilson; Li Ding
Journal:  Bioinformatics       Date:  2011-04-14       Impact factor: 6.937

3.  Making sense of missense in Lynch syndrome: the clinical perspective.

Authors:  Henry T Lynch; Thomas Jascur; Stephen Lanspa; C Richard Boland
Journal:  Cancer Prev Res (Phila)       Date:  2010-10-26

4.  Chromatid cohesion defects may underlie chromosome instability in human colorectal cancers.

Authors:  Thomas D Barber; Kirk McManus; Karen W Y Yuen; Marcelo Reis; Giovanni Parmigiani; Dong Shen; Irene Barrett; Yasaman Nouhi; Forrest Spencer; Sanford Markowitz; Victor E Velculescu; Kenneth W Kinzler; Bert Vogelstein; Christoph Lengauer; Philip Hieter
Journal:  Proc Natl Acad Sci U S A       Date:  2008-02-25       Impact factor: 11.205

5.  The (un)targeted cancer kinome.

Authors:  Oleg Fedorov; Susanne Müller; Stefan Knapp
Journal:  Nat Chem Biol       Date:  2010-03       Impact factor: 15.040

6.  A network-based kernel machine test for the identification of risk pathways in genome-wide association studies.

Authors:  Saskia Freytag; Juliane Manitz; Martin Schlather; Thomas Kneib; Christopher I Amos; Angela Risch; Jenny Chang-Claude; Joachim Heinrich; Heike Bickeböller
Journal:  Hum Hered       Date:  2014-01-14       Impact factor: 0.444

7.  Multiple genetic variants in telomere pathway genes and breast cancer risk.

Authors:  Jing Shen; Marilie D Gammon; Hui-Chen Wu; Mary Beth Terry; Qiao Wang; Patrick T Bradshaw; Susan L Teitelbaum; Alfred I Neugut; Regina M Santella
Journal:  Cancer Epidemiol Biomarkers Prev       Date:  2010-01       Impact factor: 4.254

8.  Identification of survival genes in human glioblastoma cells by small interfering RNA screening.

Authors:  Nikhil G Thaker; Fang Zhang; Peter R McDonald; Tong Ying Shun; Michael D Lewen; Ian F Pollack; John S Lazo
Journal:  Mol Pharmacol       Date:  2009-09-25       Impact factor: 4.436

9.  Modeling cancer progression via pathway dependencies.

Authors:  Elena J Edelman; Justin Guinney; Jen-Tsan Chi; Phillip G Febbo; Sayan Mukherjee
Journal:  PLoS Comput Biol       Date:  2008-02       Impact factor: 4.475

Review 10.  The breast cancer somatic 'muta-ome': tackling the complexity.

Authors:  Andrew E Teschendorff; Carlos Caldas
Journal:  Breast Cancer Res       Date:  2009-03-30       Impact factor: 6.466

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