-
1
-
-
77955508141
-
-
Available from
-
Available from: http://cancergenome.nih.gov/.
-
-
-
-
2
-
-
33947101019
-
Patterns of somatic mutation in human cancer genomes
-
DOI 10.1038/nature05610, PII NATURE05610
-
Greenman C, Stephens P, Smith R, et al. Patterns of somatic mutation in human cancer genomes. Nature 2007;446:153-8. (Pubitemid 46398669)
-
(2007)
Nature
, vol.446
, Issue.7132
, pp. 153-158
-
-
Greenman, C.1
Stephens, P.2
Smith, R.3
Dalgliesh, G.L.4
Hunter, C.5
Bignell, G.6
Davies, H.7
Teague, J.8
Butler, A.9
Stevens, C.10
Edkins, S.11
O'Meara, S.12
Vastrik, I.13
Schmidt, E.E.14
Avis, T.15
Barthorpe, S.16
Bhamra, G.17
Buck, G.18
Choudhury, B.19
Clements, J.20
Cole, J.21
Dicks, E.22
Forbes, S.23
Gray, K.24
Halliday, K.25
Harrison, R.26
Hills, K.27
Hinton, J.28
Jenkinson, A.29
Jones, D.30
Menzies, A.31
Mironenko, T.32
Perry, J.33
Raine, K.34
Richardson, D.35
Shepherd, R.36
Small, A.37
Tofts, C.38
Varian, J.39
Webb, T.40
West, S.41
Widaa, S.42
Yates, A.43
Cahill, D.P.44
Louis, D.N.45
Goldstraw, P.46
Nicholson, A.G.47
Brasseur, F.48
Looijenga, L.49
Weber, B.L.50
Chiew, Y.-E.51
DeFazio, A.52
Greaves, M.F.53
Green, A.R.54
Campbell, P.55
Birney, E.56
Easton, D.F.57
Chenevix-Trench, G.58
Tan, M.-H.59
Khoo, S.K.60
Teh, B.T.61
Yuen, S.T.62
Leung, S.Y.63
Wooster, R.64
Futreal, P.A.65
Stratton, M.R.66
more..
-
3
-
-
52149123619
-
Core signaling pathways in human pancreatic cancers revealed by global genomic analyses
-
Jones S, Zhang X, Parsons DW, et al. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 2008;321:1801-6.
-
(2008)
Science
, vol.321
, pp. 1801-1806
-
-
Jones, S.1
Zhang, X.2
Parsons, D.W.3
-
4
-
-
52949127312
-
An integrated genomic analysis of human glioblastoma multiforme
-
Parsons DW, Jones S, Zhang X, et al. An integrated genomic analysis of human glioblastoma multiforme. Science 2008;321:1807-12.
-
(2008)
Science
, vol.321
, pp. 1807-1812
-
-
Parsons, D.W.1
Jones, S.2
Zhang, X.3
-
5
-
-
33749993417
-
The consensus coding sequences of human breast and colorectal cancers
-
Sjoblom T, Jones S, Wood LD, et al. The consensus coding sequences of human breast and colorectal cancers. Science 2006;314:268-74.
-
(2006)
Science
, vol.314
, pp. 268-274
-
-
Sjoblom, T.1
Jones, S.2
Wood, L.D.3
-
6
-
-
54549094903
-
Somatic mutations affect key pathways in lung adenocarcinoma
-
Ding L, Getz G, Wheeler DA, et al. Somatic mutations affect key pathways in lung adenocarcinoma. Nature 2008;455:1069-75.
-
(2008)
Nature
, vol.455
, pp. 1069-1075
-
-
Ding, L.1
Getz, G.2
Wheeler, D.A.3
-
7
-
-
33747869580
-
Statistical analysis of pathogenicity of somatic mutations in cancer
-
Greenman C, Wooster R, Futreal PA, Stratton MR, Easton DF. Statistical analysis of pathogenicity of somatic mutations in cancer. Genetics 2006;173:2187-98.
-
(2006)
Genetics
, vol.173
, pp. 2187-2198
-
-
Greenman, C.1
Wooster, R.2
Futreal, P.A.3
Stratton, M.R.4
Easton, D.F.5
-
8
-
-
0242318328
-
Likelihood Models of Somatic Mutation and Codon Substitution in Cancer Genes
-
Yang Z, Ro S, Rannala B. Likelihood models of somatic mutation and codon substitution in cancer genes. Genetics 2003;165:695-705. (Pubitemid 37337636)
-
(2003)
Genetics
, vol.165
, Issue.2
, pp. 695-705
-
-
Yang, Z.1
Ro, S.2
Rannala, B.3
-
9
-
-
43149084575
-
Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks
-
Uren AG, Kool J, Matentzoglu K, et al. Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks. Cell 2008;133:727-41.
-
(2008)
Cell
, vol.133
, pp. 727-741
-
-
Uren, A.G.1
Kool, J.2
Matentzoglu, K.3
-
10
-
-
33847293670
-
High-throughput oncogene mutation profiling in human cancer
-
Thomas RK, Baker AC, Debiasi RM, et al. High-throughput oncogene mutation profiling in human cancer. Nat Genet 2007;39:347-51.
-
(2007)
Nat Genet
, vol.39
, pp. 347-351
-
-
Thomas, R.K.1
Baker, A.C.2
Debiasi, R.M.3
-
11
-
-
4043181214
-
Cancer genes and the pathways they control
-
DOI 10.1038/nm1087
-
Vogelstein B, Kinzler KW. Cancer genes and the pathways they control. Nat Med 2004;10:789-99. (Pubitemid 39070849)
-
(2004)
Nature Medicine
, vol.10
, Issue.8
, pp. 789-799
-
-
Vogelstein, B.1
Kinzler, K.W.2
-
12
-
-
54549108740
-
Comprehensive genomic characterization defines human glioblastoma genes and core pathways
-
TCGA-Consortium
-
TCGA-Consortium. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 2008;455:1061-8.
-
(2008)
Nature
, vol.455
, pp. 1061-1068
-
-
-
13
-
-
36248962105
-
The genomic landscapes of human breast and colorectal cancers
-
Wood LD, Parsons DW, Jones S, et al. The genomic landscapes of human breast and colorectal cancers. Science 2007;318:1108-13.
-
(2007)
Science
, vol.318
, pp. 1108-1113
-
-
Wood, L.D.1
Parsons, D.W.2
Jones, S.3
-
14
-
-
34548388340
-
A multidimensional analysis of genes mutated in breast and colorectal cancers
-
Lin J, Gan CM, Zhang X, et al. A multidimensional analysis of genes mutated in breast and colorectal cancers. Genome Res 2007;17:1304-18.
-
(2007)
Genome Res
, vol.17
, pp. 1304-1318
-
-
Lin, J.1
Gan, C.M.2
Zhang, X.3
-
15
-
-
48749118242
-
Combinatorial patterns of somatic gene mutations in cancer
-
Yeang CH, McCormick F, Levine A. Combinatorial patterns of somatic gene mutations in cancer. FASEB J 2008;22:2605-22.
-
(2008)
FASEB J
, vol.22
, pp. 2605-2622
-
-
Yeang, C.H.1
McCormick, F.2
Levine, A.3
-
16
-
-
3843084078
-
The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website
-
Bamford S, Dawson E, Forbes S, et al. The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. Br J Cancer 2004;91:355-8.
-
(2004)
Br J Cancer
, vol.91
, pp. 355-358
-
-
Bamford, S.1
Dawson, E.2
Forbes, S.3
-
17
-
-
0033982936
-
KEGG: Kyoto Encyclopedia of Genes and Genomes
-
Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000;28:27-30. (Pubitemid 30047706)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
18
-
-
77955475822
-
-
Available from
-
Available from: http://www.biocarta.com/.
-
-
-
-
19
-
-
34848827433
-
Comparing classical pathways and modern networks: Towards the development of an edge ontology
-
Lu LJ, Sboner A, Huang YJ, et al. Comparing classical pathways and modern networks: towards the development of an edge ontology. Trends Biochem Sci 2007;32:320-31.
-
(2007)
Trends Biochem Sci
, vol.32
, pp. 320-331
-
-
Lu, L.J.1
Sboner, A.2
Huang, Y.J.3
-
20
-
-
0034069495
-
Gene ontology: Tool for the unification of biology
-
The Gene Ontology Consortium
-
Ashburner M, Ball CA, Blake JA, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000;25:25-9.
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
-
21
-
-
10744224197
-
Development of human protein reference database as an initial platform for approaching systems biology in humans
-
Peri S, Navarro JD, Amanchy R, et al. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res 2003;13:2363-71.
-
(2003)
Genome Res
, vol.13
, pp. 2363-2371
-
-
Peri, S.1
Navarro, J.D.2
Amanchy, R.3
-
22
-
-
77955493382
-
-
Available from
-
Available from: http://www.biocarta.com/genes/allPathways.asp.
-
-
-
-
23
-
-
77955492638
-
-
Available from
-
Available from: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/.
-
-
-
-
24
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 1995:289-300.
-
(1995)
J R Stat Soc B
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
25
-
-
70350451926
-
A new multitest correction (SGoF) that increases its statistical power when increasing the number of tests
-
Carvajal-Rodriguez A, de Una-Alvarez J, Rolan-Alvarez E. A new multitest correction (SGoF) that increases its statistical power when increasing the number of tests. BMC Bioinformatics 2009;10:209.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 209
-
-
Carvajal-Rodriguez, A.1
De Una-Alvarez, J.2
Rolan-Alvarez, E.3
-
27
-
-
77955496758
-
-
Available from
-
Available from: http://cneurocvs.rmki.kfki.hu/igraph.
-
-
-
-
28
-
-
0037174670
-
Network motifs: Simple building blocks of complex networks
-
DOI 10.1126/science.298.5594.824
-
Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U. Network motifs: simple building blocks of complex networks. Science 2002;298:824-7. (Pubitemid 35231534)
-
(2002)
Science
, vol.298
, Issue.5594
, pp. 824-827
-
-
Milo, R.1
Shen-Orr, S.2
Itzkovitz, S.3
Kashtan, N.4
Chklovskii, D.5
Alon, U.6
-
31
-
-
0034614637
-
The hallmarks of cancer
-
Hanahan D, Weinberg RA. The hallmarks of cancer. Cell 2000;100:57-70.
-
(2000)
Cell
, vol.100
, pp. 57-70
-
-
Hanahan, D.1
Weinberg, R.A.2
-
32
-
-
0037461932
-
DLC-1 gene inhibits human breast cancer cell growth and in vivo tumorigenicity
-
Yuan BZ, Zhou X, Durkin ME, et al. DLC-1 gene inhibits human breast cancer cell growth and in vivo tumorigenicity. Oncogene 2003;22:445-50.
-
(2003)
Oncogene
, vol.22
, pp. 445-450
-
-
Yuan, B.Z.1
Zhou, X.2
Durkin, M.E.3
-
33
-
-
0036342469
-
Expression of Wnt ligands and Frizzled receptors in colonic mucosa and in colon carcinoma
-
Holcombe RF, Marsh JL, Waterman ML, Lin F, Milovanovic T, Truong T. Expression of Wnt ligands and Frizzled receptors in colonic mucosa and in colon carcinoma. Mol Pathol 2002;55:220-6.
-
(2002)
Mol Pathol
, vol.55
, pp. 220-226
-
-
Holcombe, R.F.1
Marsh, J.L.2
Waterman, M.L.3
Lin, F.4
Milovanovic, T.5
Truong, T.6
-
34
-
-
17144452027
-
Short postoperative survival for glioblastoma patients with a dysfunctional Rb1 pathway in combination with no wild-type PTEN
-
Backlund LM, Nilsson BR, Goike HM, et al. Short postoperative survival for glioblastoma patients with a dysfunctional Rb1 pathway in combination with no wild-type PTEN. Clin Cancer Res 2003;9:4151-8.
-
(2003)
Clin Cancer Res
, vol.9
, pp. 4151-4158
-
-
Backlund, L.M.1
Nilsson, B.R.2
Goike, H.M.3
-
35
-
-
0036791030
-
Growth suppression of human carcinoma cells by reintroduction of the p300 coactivator
-
Suganuma T, Kawabata M, Ohshima T, Ikeda MA. Growth suppression of human carcinoma cells by reintroduction of the p300 coactivator. Proc Natl Acad Sci U S A 2002;99:13073-8.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 13073-13078
-
-
Suganuma, T.1
Kawabata, M.2
Ohshima, T.3
Ikeda, M.A.4
-
36
-
-
2542462086
-
Gene expression in gastrointestinal stromal tumors is distinguished by KIT genotype and anatomic site
-
Antonescu CR, Viale A, Sarran L, et al. Gene expression in gastrointestinal stromal tumors is distinguished by KIT genotype and anatomic site. Clin Cancer Res 2004;10:3282-90.
-
(2004)
Clin Cancer Res
, vol.10
, pp. 3282-3290
-
-
Antonescu, C.R.1
Viale, A.2
Sarran, L.3
-
37
-
-
44349177548
-
CaV3.2 T-type calcium channels are involved in calcium-dependent secretion of neuroendocrine prostate cancer cells
-
Gackiere F, Bidaux G, Delcourt P, et al. CaV3.2 T-type calcium channels are involved in calcium-dependent secretion of neuroendocrine prostate cancer cells. J Biol Chem 2008;283:10162-73.
-
(2008)
J Biol Chem
, vol.283
, pp. 10162-10173
-
-
Gackiere, F.1
Bidaux, G.2
Delcourt, P.3
-
38
-
-
33644641087
-
The role of type IV collagen and basement membranes in cancer progression and metastasis
-
DOI 10.2353/ajpath.2006.051321
-
Tanjore H, Kalluri R. The role of type IV collagen and basement membranes in cancer progression and metastasis. Am J Pathol 2006;168:715-7. (Pubitemid 43327723)
-
(2006)
American Journal of Pathology
, vol.168
, Issue.3
, pp. 715-717
-
-
Tanjore, H.1
Kalluri, R.2
-
39
-
-
0031262009
-
Neuronal differentiation of human small cell lung cancer cell line PC-6 by Solcoseryl
-
Shimizu T. Neuronal differentiation of human small cell lung cancer cell line PC-6 by Solcoseryl. Hokkaido Igaku Zasshi 1997;72:621-33.
-
(1997)
Hokkaido Igaku Zasshi
, vol.72
, pp. 621-633
-
-
Shimizu, T.1
-
40
-
-
69749086899
-
Identification of rare cancer driver mutations by network reconstruction
-
Torkamani A, Schork NJ. Identification of rare cancer driver mutations by network reconstruction. Genome Res 2009;19:1570-8.
-
(2009)
Genome Res
, vol.19
, pp. 1570-1578
-
-
Torkamani, A.1
Schork, N.J.2
-
41
-
-
34548677928
-
Comment on "The consensus coding sequences of human breast and colorectal cancers"
-
Getz G, Hofling H, Mesirov JP, et al. Comment on "The consensus coding sequences of human breast and colorectal cancers". Science 2007;317:1500.
-
(2007)
Science
, vol.317
, pp. 1500
-
-
Getz, G.1
Hofling, H.2
Mesirov, J.P.3
-
43
-
-
36448946146
-
Improved detection of overrepresentation of Gene-Ontology annotations with parent-child analysis
-
DOI 10.1093/bioinformatics/btm440
-
Grossmann S, Bauer S, Robinson PN, Vingron M. Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis. Bioinformatics (Oxford, England) 2007;23:3024-31. (Pubitemid 350162867)
-
(2007)
Bioinformatics
, vol.23
, Issue.22
, pp. 3024-3031
-
-
Grossmann, S.1
Bauer, S.2
Robinson, P.N.3
Vingron, M.4
-
44
-
-
33745626459
-
Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
-
Oxford, England
-
Alexa A, Rahnenfuhrer J, Lengauer T. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics (Oxford, England) 2006;22:1600-7.
-
(2006)
Bioinformatics
, vol.22
, pp. 1600-1607
-
-
Alexa, A.1
Rahnenfuhrer, J.2
Lengauer, T.3
-
45
-
-
67649205714
-
Evaluating reproducibility of differential expression discoveries in microarray studies by considering correlated molecular changes
-
Zhang M, Zhang L, Zou J, et al. Evaluating reproducibility of differential expression discoveries in microarray studies by considering correlated molecular changes. Bioinformatics 2009;25:1662-8.
-
(2009)
Bioinformatics
, vol.25
, pp. 1662-1668
-
-
Zhang, M.1
Zhang, L.2
Zou, J.3
-
46
-
-
34548583420
-
Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network
-
Guo Z, Li Y, Gong X, et al. Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network. Bioinformatics 2007;23:2121-8.
-
(2007)
Bioinformatics
, vol.23
, pp. 2121-2128
-
-
Guo, Z.1
Li, Y.2
Gong, X.3
-
47
-
-
22844450110
-
Systematic interpretation of genetic interactions using protein networks
-
DOI 10.1038/nbt1096
-
Kelley R, Ideker T. Systematic interpretation of genetic interactions using protein networks. Nat Biotechnol 2005;23:561-6. (Pubitemid 41724894)
-
(2005)
Nature Biotechnology
, vol.23
, Issue.5
, pp. 561-566
-
-
Kelley, R.1
Ideker, T.2
-
48
-
-
34548024598
-
Integrating physical and genetic maps: From genomes to interaction networks
-
DOI 10.1038/nrg2144, PII NRG2144
-
Beyer A, Bandyopadhyay S, Ideker T. Integrating physical and genetic maps: from genomes to interaction networks. Nat Rev Genet 2007;8:699-710. (Pubitemid 47281988)
-
(2007)
Nature Reviews Genetics
, vol.8
, Issue.9
, pp. 699-710
-
-
Beyer, A.1
Bandyopadhyay, S.2
Ideker, T.3
-
49
-
-
34247193051
-
Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks
-
DOI 10.1038/msb4100144, PII MSB4100144
-
Ulitsky I, Shamir R. Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks. Mol Syst Biol 2007;3:104. (Pubitemid 46625178)
-
(2007)
Molecular Systems Biology
, vol.3
, pp. 104
-
-
Ulitsky, I.1
Shamir, R.2
-
50
-
-
77949532152
-
Extracting consistent knowledge from highly inconsistent cancer gene data sources
-
Gong X, Wu R, Zhang Y, et al. Extracting consistent knowledge from highly inconsistent cancer gene data sources. BMC Bioinformatics 2010;11:76.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 76
-
-
Gong, X.1
Wu, R.2
Zhang, Y.3
-
51
-
-
77955502777
-
-
Available from
-
Available from: http://bioinfo.hrbmu.edu.cn/fcensus/.
-
-
-
-
52
-
-
33847005866
-
Limits to the Human Cancer Genome Project?
-
Strauss BS. Limits to the Human Cancer Genome Project? Science 2007;315:762-4.
-
(2007)
Science
, vol.315
, pp. 762-764
-
-
Strauss, B.S.1
-
54
-
-
0242490780
-
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
-
DOI 10.1101/gr.1239303
-
Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003;13:2498-504. (Pubitemid 37428274)
-
(2003)
Genome Research
, vol.13
, Issue.11
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
|