-
1
-
-
34250887474
-
Taking gene-expression profiling to the clinic: When will molecular signatures become relevant to patient care?
-
10.1038/nrc2173 17585334
-
Sotiriou C Piccart MJ Taking gene-expression profiling to the clinic: when will molecular signatures become relevant to patient care? Nat Rev Cancer 2007, 7:545-553. 10.1038/nrc2173 17585334
-
(2007)
Nat Rev Cancer
, vol.7
, pp. 545-553
-
-
Sotiriou, C.1
Piccart, M.J.2
-
2
-
-
54849425774
-
Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells
-
2572072 18823535 10.1186/1471-2105-9-404
-
Niida A Smith AD Imoto S Tsutsumi S Aburatani H Zhang MQ Akiyama T Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells BMC Bioinformatics 9, 404. 2572072 18823535 10.1186/1471-2105-9-404
-
BMC Bioinformatics
, vol.9
, pp. 404
-
-
Niida, A.1
Smith, A.D.2
Imoto, S.3
Tsutsumi, S.4
Aburatani, H.5
Zhang, M.Q.6
Akiyama, T.7
-
3
-
-
0032441150
-
Cluster analysis and display of genome-wide expression patterns
-
9843981 10.1073/pnas.95.25.14863
-
Eisen MB Spellman PT Brown PO Botstein D Cluster analysis and display of genome-wide expression patterns Proc Natl Acad Sci USA 1998, 95:14863-14868. 24541 9843981 10.1073/pnas.95.25.14863
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 14863-14868
-
-
Eisen, M.B.1
Spellman, P.T.2
Brown, P.O.3
Botstein, D.4
-
4
-
-
1942453302
-
Predicting gene expression from sequence
-
10.1016/S0092-8674(04)00304-6 15084257
-
Beer MA Tavazoie S Predicting gene expression from sequence Cell 2004, 117:185-198. 10.1016/S0092-8674(04)00304-6 15084257
-
(2004)
Cell
, vol.117
, pp. 185-198
-
-
Beer, M.A.1
Tavazoie, S.2
-
5
-
-
10744226222
-
Computational discovery of gene modules and regulatory networks
-
10.1038/nbt890 14555958
-
Bar-Joseph Z Gerber GK Lee TI Rinaldi NJ Yoo JY Robert F Gordon DB Fraenkel E Jaakkola TS Young RA Gifford DK Computational discovery of gene modules and regulatory networks Nat Biotechnol 2003, 21:1337-1342. 10.1038/nbt890 14555958
-
(2003)
Nat Biotechnol
, vol.21
, pp. 1337-1342
-
-
Bar-Joseph, Z.1
Gerber, G.K.2
Lee, T.I.3
Rinaldi, N.J.4
Yoo, J.Y.5
Robert, F.6
Gordon, D.B.7
Fraenkel, E.8
Jaakkola, T.S.9
Young, R.A.10
Gifford, D.K.11
-
6
-
-
34447555782
-
Mining gene expression profiles: Expression signatures as cancer phenotypes
-
10.1038/nrg2137 17607306
-
Nevins JR Potti A Mining gene expression profiles: Expression signatures as cancer phenotypes Nat Rev Genet 2007, 8:601-609. 10.1038/nrg2137 17607306
-
(2007)
Nat Rev Genet
, vol.8
, pp. 601-609
-
-
Nevins, J.R.1
Potti, A.2
-
7
-
-
20044388557
-
From signatures to models: Understanding cancer using microarrays
-
10.1038/ng1561
-
Segal E Friedman N Kaminski N Regev A Koller D From signatures to models: Understanding cancer using microarrays Nat Genet 37 2005, (Suppl):S38-S45. 10.1038/ng1561
-
(2005)
Nat Genet
, vol.37
, Issue.SUPPL.
-
-
Segal, E.1
Friedman, N.2
Kaminski, N.3
Regev, A.4
Koller, D.5
-
8
-
-
33644876958
-
TRANSFAC and its module TRANSCompel: Transcriptional gene regulation in eukaryotes
-
1347505 16381825 10.1093/nar/gkj143
-
Matys V Kel-Margoulis OV Fricke E Liebich I Land S Barre-Dirrie A Reuter I Chekmenev D Krull M Hornischer K Voss N Stegmaier P Lewicki-Potapov B Saxel H Kel AE Wingender E TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes Nucleic Acids Res 2006, 34:D108-D110. 1347505 16381825 10.1093/nar/gkj143
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Matys, V.1
Kel-Margoulis, O.V.2
Fricke, E.3
Liebich, I.4
Land, S.5
Barre-Dirrie, A.6
Reuter, I.7
Chekmenev, D.8
Krull, M.9
Hornischer, K.10
Voss, N.11
Stegmaier, P.12
Lewicki-Potapov, B.13
Saxel, H.14
Kel, A.E.15
Wingender, E.16
-
9
-
-
33644875782
-
A new generation of JASPAR, the open-access repository for transcription factor binding site profiles
-
1347477 16381983 10.1093/nar/gkj115
-
Vlieghe D Sandelin A De Bleser PJ Vleminckx K Wasserman WW van Roy F Lenhard B A new generation of JASPAR, the open-access repository for transcription factor binding site profiles Nucleic Acids Res 2006, 34:D95- D97. 1347477 16381983 10.1093/nar/gkj115
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Vlieghe, D.1
Sandelin, A.2
De Bleser, P.J.3
Vleminckx, K.4
Wasserman, W.W.5
van Roy, F.6
Lenhard, B.7
-
10
-
-
33750442923
-
Genome-wide analysis of estrogen receptor binding sites
-
10.1038/ng1901 17013392
-
Carroll JS Meyer CA Song J Li W Geistlinger TR Eeckhoute J Brodsky AS Keeton EK Fertuck KC Hall GF Wang Q Bekiranov S Sementchenko V Fox EA Silver PA Gingeras TR Liu XS Brown M Genome-wide analysis of estrogen receptor binding sites Nat Genet 2006, 38:1289-1297. 10.1038/ng1901 17013392
-
(2006)
Nat Genet
, vol.38
, pp. 1289-1297
-
-
Carroll, J.S.1
Meyer, C.A.2
Song, J.3
Li, W.4
Geistlinger, T.R.5
Eeckhoute, J.6
Brodsky, A.S.7
Keeton, E.K.8
Fertuck, K.C.9
Hall, G.F.10
Wang, Q.11
Bekiranov, S.12
Sementchenko, V.13
Fox, E.A.14
Silver, P.A.15
Gingeras, T.R.16
Liu, X.S.17
Brown, M.18
-
11
-
-
33645809747
-
Coordinated binding of NF-kappaB family members in the response of human cells to lipopolysaccharide
-
1426243 16595631 10.1073/pnas.0510996103
-
Schreiber J Jenner RG Murray HL Gerber GK Gifford DK Young RA Coordinated binding of NF-kappaB family members in the response of human cells to lipopolysaccharide Proc Natl Acad Sci USA 2006, 103:5899-5904. 1426243 16595631 10.1073/pnas.0510996103
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 5899-5904
-
-
Schreiber, J.1
Jenner, R.G.2
Murray, H.L.3
Gerber, G.K.4
Gifford, D.K.5
Young, R.A.6
-
12
-
-
33646865180
-
Control of developmental regulators by Polycomb in human embryonic stem cells
-
10.1016/j.cell.2006.02.043 16630818
-
Lee TI Jenner RG Boyer LA Guenther MG Levine SS Kumar RM Chevalier B Johnstone SE Cole MF Isono K Koseki H Fuchikami T Abe K Murray HL Zucker JP Yuan B Bell GW Herbolsheimer E Hannett NM Sun K Odom DT Otte AP Volkert TL Bartel DP Melton DA Gifford DK Jaenisch R Young RA Control of developmental regulators by Polycomb in human embryonic stem cells Cell 2006, 125:301-313. 10.1016/j.cell.2006.02.043 16630818
-
(2006)
Cell
, vol.125
, pp. 301-313
-
-
Lee, T.I.1
Jenner, R.G.2
Boyer, L.A.3
Guenther, M.G.4
Levine, S.S.5
Kumar, R.M.6
Chevalier, B.7
Johnstone, S.E.8
Cole, M.F.9
Isono, K.10
Koseki, H.11
Fuchikami, T.12
Abe, K.13
Murray, H.L.14
Zucker, J.P.15
Yuan, B.16
Bell, G.W.17
Herbolsheimer, E.18
Hannett, N.M.19
Sun, K.20
Odom, D.T.21
Otte, A.P.22
Volkert, T.L.23
Bartel, D.P.24
Melton, D.A.25
Gifford, D.K.26
Jaenisch, R.27
Young, R.A.28
more..
-
13
-
-
33745456986
-
Core transcriptional regulatory circuitry in human hepatocytes
-
1681491 16738562 10.1038/msb4100059
-
Odom DT Dowell RD Jacobsen ES Nekludova L Rolfe PA Danford TW Gifford DK Fraenkel E Bell GI Young RA Core transcriptional regulatory circuitry in human hepatocytes Mol Syst Biol 2006, 2:0017. 1681491 16738562 10.1038/ msb4100059
-
(2006)
Mol Syst Biol
, vol.2
, pp. 0017
-
-
Odom, D.T.1
Dowell, R.D.2
Jacobsen, E.S.3
Nekludova, L.4
Rolfe, P.A.5
Danford, T.W.6
Gifford, D.K.7
Fraenkel, E.8
Bell, G.I.9
Young, R.A.10
-
14
-
-
30344478870
-
A global map of p53 transcription-factor binding sites in the human genome
-
10.1016/j.cell.2005.10.043 16413492
-
Wei CL Wu Q Vega VB Chiu KP Ng P Zhang T Shahab A Yong HC Fu Y Weng Z Liu J Zhao XD Chew JL Lee YL Kuznetsov VA Sung WK Miller LD Lim B Liu ET Yu Q Ng HH Ruan Y A global map of p53 transcription-factor binding sites in the human genome Cell 2006, 124:207-219. 10.1016/j.cell.2005.10.043 16413492
-
(2006)
Cell
, vol.124
, pp. 207-219
-
-
Wei, C.L.1
Wu, Q.2
Vega, V.B.3
Chiu, K.P.4
Ng, P.5
Zhang, T.6
Shahab, A.7
Yong, H.C.8
Fu, Y.9
Weng, Z.10
Liu, J.11
Zhao, X.D.12
Chew, J.L.13
Lee, Y.L.14
Kuznetsov, V.A.15
Sung, W.K.16
Miller, L.D.17
Lim, B.18
Liu, E.T.19
Yu, Q.20
Ng, H.H.21
Ruan, Y.22
more..
-
15
-
-
13844250828
-
Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors
-
130569 12297621 10.1073/pnas.162471999
-
Pollack JR Sorlie T Perou CM Rees CA Jeffrey SS Lonning PE Tibshirani R Botstein D Borresen-Dale AL Brown PO Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors Proc Natl Acad Sci USA 2002, 99:12963-12968. 130569 12297621 10.1073/pnas.162471999
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 12963-12968
-
-
Pollack, J.R.1
Sorlie, T.2
Perou, C.M.3
Rees, C.A.4
Jeffrey, S.S.5
Lonning, P.E.6
Tibshirani, R.7
Botstein, D.8
Borresen-Dale, A.L.9
Brown, P.O.10
-
16
-
-
26444546442
-
An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival
-
1197273 16141321 10.1073/pnas.0506230102
-
Miller LD Smeds J George J Vega VB Vergara L Ploner A Pawitan Y Hall P Klaar S Liu ET Bergh J An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival Proc Natl Acad Sci USA 2005, 102:13550-13555. 1197273 16141321 10.1073/pnas.0506230102
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 13550-13555
-
-
Miller, L.D.1
Smeds, J.2
George, J.3
Vega, V.B.4
Vergara, L.5
Ploner, A.6
Pawitan, Y.7
Hall, P.8
Klaar, S.9
Liu, E.T.10
Bergh, J.11
-
17
-
-
33745128746
-
Inferring transcriptional modules from ChIP-chip, motif and microarray data
-
1779513 16677396 10.1186/gb-2006-7-5-r37
-
Lemmens K Dhollander T De Bie T Monsieurs P Engelen K Smets B Winderickx J De Moor B Marchal K Inferring transcriptional modules from ChIP-chip, motif and microarray data Genome Biol 2006, 7:R37. 1779513 16677396 10.1186/gb-2006-7-5-r37
-
(2006)
Genome Biol
, vol.7
-
-
Lemmens, K.1
Dhollander, T.2
De Bie, T.3
Monsieurs, P.4
Engelen, K.5
Smets, B.6
Winderickx, J.7
De Moor, B.8
Marchal, K.9
-
18
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
1239896 16199517 10.1073/pnas.0506580102
-
Subramanian A Tamayo P Mootha VK Mukherjee S Ebert BL Gillette MA Paulovich A Pomeroy SL Golub TR Lander ES Mesirov JP Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles Proc Natl Acad Sci USA 2005, 102:15545-15550. 1239896 16199517 10.1073/pnas.0506580102
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
Mukherjee, S.4
Ebert, B.L.5
Gillette, M.A.6
Paulovich, A.7
Pomeroy, S.L.8
Golub, T.R.9
Lander, E.S.10
Mesirov, J.P.11
-
19
-
-
0034730140
-
Singular value decomposition for genome-wide expression data processing and modeling
-
27718 10963673 10.1073/pnas.97.18.10101
-
Alter O Brown PO Botstein D Singular value decomposition for genome-wide expression data processing and modeling Proc Natl Acad Sci USA 2000, 97:10101-10106. 27718 10963673 10.1073/pnas.97.18.10101
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 10101-10106
-
-
Alter, O.1
Brown, P.O.2
Botstein, D.3
-
20
-
-
34347219009
-
Metagene projection for cross-platform, cross-species characterization of global transcriptional states
-
1838404 17389406 10.1073/pnas.0701068104
-
Tamayo P Scanfeld D Ebert BL Gillette MA Roberts CW Mesirov JP Metagene projection for cross-platform, cross-species characterization of global transcriptional states Proc Natl Acad Sci USA 2007, 104:5959-5964. 1838404 17389406 10.1073/pnas.0701068104
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 5959-5964
-
-
Tamayo, P.1
Scanfeld, D.2
Ebert, B.L.3
Gillette, M.A.4
Roberts, C.W.5
Mesirov, J.P.6
-
22
-
-
29144442380
-
Multi-way clustering of microarray data using probabilistic sparse matrix factorization
-
10.1093/bioinformatics/bti1041
-
Dueck D Morris QD Frey BJ Multi-way clustering of microarray data using probabilistic sparse matrix factorization Bioinformatics Suppl 2005, 1:i144-i151. 10.1093/bioinformatics/bti1041
-
(2005)
Bioinformatics Suppl
, vol.1
-
-
Dueck, D.1
Morris, Q.D.2
Frey, B.J.3
-
23
-
-
0037810449
-
Subsystem identification through dimensionality reduction of large-scale gene expression data
-
403744 12840046 10.1101/gr.903503
-
Kim PM Tidor B Subsystem identification through dimensionality reduction of large-scale gene expression data Genome Res 2003, 13:1706-1718. 403744 12840046 10.1101/gr.903503
-
(2003)
Genome Res
, vol.13
, pp. 1706-1718
-
-
Kim, P.M.1
Tidor, B.2
-
24
-
-
0032729435
-
Exploring expression data: Identification and analysis of coexpressed genes
-
310826 10568750 10.1101/gr.9.11.1106
-
Heyer LJ Kruglyak S Yooseph S Exploring expression data: Identification and analysis of coexpressed genes Genome Res 1999, 9:1106-1115. 310826 10568750 10.1101/gr.9.11.1106
-
(1999)
Genome Res
, vol.9
, pp. 1106-1115
-
-
Heyer, L.J.1
Kruglyak, S.2
Yooseph, S.3
-
25
-
-
0036080361
-
Adaptive quality-based clustering of gene expression profiles
-
10.1093/bioinformatics/18.5.735 12050070
-
De Smet F Mathys J Marchal K Thijs G De Moor B Moreau Y Adaptive quality-based clustering of gene expression profiles Bioinformatics 2002, 18:735-746. 10.1093/bioinformatics/18.5.735 12050070
-
(2002)
Bioinformatics
, vol.18
, pp. 735-746
-
-
De Smet, F.1
Mathys, J.2
Marchal, K.3
Thijs, G.4
De Moor, B.5
Moreau, Y.6
-
26
-
-
15244358503
-
Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals
-
10.1038/nature03441 15735639
-
Xie X Lu J Kulbokas EJ Golub TR Mootha V Lindblad-Toh K Lander ES Kellis M Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals Nature 2005, 434:338-345. 10.1038/nature03441 15735639
-
(2005)
Nature
, vol.434
, pp. 338-345
-
-
Xie, X.1
Lu, J.2
Kulbokas, E.J.3
Golub, T.R.4
Mootha, V.5
Lindblad-Toh, K.6
Lander, E.S.7
Kellis, M.8
-
27
-
-
33847172748
-
Statistical significance of cis-regulatory modules
-
1796902 17241466 10.1186/1471-2105-8-19
-
Schones DE Smith AD Zhang MQ Statistical significance of cis-regulatory modules BMC Bioinformatics 2007, 8:19. 1796902 17241466 10.1186/ 1471-2105-8-19
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 19
-
-
Schones, D.E.1
Smith, A.D.2
Zhang, M.Q.3
-
28
-
-
12344269924
-
GO::TermFinder?open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
-
10.1093/bioinformatics/bth456 15297299
-
Boyle EI Weng S Gollub J Jin H Botstein D Cherry JM Sherlock G GO::TermFinder?open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes Bioinformatics 2004, 20:3710-3715. 10.1093/bioinformatics/bth456 15297299
-
(2004)
Bioinformatics
, vol.20
, pp. 3710-3715
-
-
Boyle, E.I.1
Weng, S.2
Gollub, J.3
Jin, H.4
Botstein, D.5
Cherry, J.M.6
Sherlock, G.7
-
29
-
-
10744224197
-
Development of human protein reference database as an initial platform for approaching systems biology in humans
-
403728 14525934 10.1101/gr.1680803
-
Peri S Navarro JD Amanchy R Kristiansen TZ Jonnalagadda CK Surendranath V Niranjan V Muthusamy B Gandhi TK Gronborg M Ibarrola N Deshpande N Shanker K Shivashankar HN Rashmi BP Ramya MA Zhao Z Chandrika KN Padma N Harsha HC Yatish AJ Kavitha MP Menezes M Choudhury DR Suresh S Ghosh N Saravana R Chandran S Krishna S Joy M Anand SK Madavan V Joseph A Wong GW Schiemann WP Constantinescu SN Huang L Khosravi-Far R Steen H Tewari M Ghaffari S Blobe GC Dang CV Garcia JG Pevsner J Jensen ON Roepstorff P Deshpande KS Chinnaiyan AM Hamosh A Chakravarti A Pandey A Development of human protein reference database as an initial platform for approaching systems biology in humans Genome Res 2003, 13:2363-2371. 403728 14525934 10.1101/gr.1680803
-
(2003)
Genome Res
, vol.13
, pp. 2363-2371
-
-
Peri, S.1
Navarro, J.D.2
Amanchy, R.3
Kristiansen, T.Z.4
Jonnalagadda, C.K.5
Surendranath, V.6
Niranjan, V.7
Muthusamy, B.8
Gandhi, T.K.9
Gronborg, M.10
Ibarrola, N.11
Deshpande, N.12
Shanker, K.13
Shivashankar, H.N.14
Rashmi, B.P.15
Ramya, M.A.16
Zhao, Z.17
Chandrika, K.N.18
Padma, N.19
Harsha, H.C.20
Yatish, A.J.21
Kavitha, M.P.22
Menezes, M.23
Choudhury, D.R.24
Suresh, S.25
Ghosh, N.26
Saravana, R.27
Chandran, S.28
Krishna, S.29
Joy, M.30
Anand, S.K.31
Madavan, V.32
Joseph, A.33
Wong, G.W.34
Schiemann, W.P.35
Constantinescu, S.N.36
Huang, L.37
Khosravi-Far, R.38
Steen, H.39
Tewari, M.40
Ghaffari, S.41
Blobe, G.C.42
Dang, C.V.43
Garcia, J.G.44
Pevsner, J.45
Jensen, O.N.46
Roepstorff, P.47
Deshpande, K.S.48
Chinnaiyan, A.M.49
Hamosh, A.50
Chakravarti, A.51
Pandey, A.52
more..
-
30
-
-
0242490780
-
Cytoscape: A software environment for integrated models of biomolecular interaction networks
-
403769 14597658 10.1101/gr.1239303
-
Shannon P Markiel A Ozier O Baliga NS Wang JT Ramage D Amin N Schwikowski B Ideker T Cytoscape: A software environment for integrated models of biomolecular interaction networks Genome Res 2003, 13:2498-504. 403769 14597658 10.1101/gr.1239303
-
(2003)
Genome Res
, vol.13
, 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
-
31
-
-
33845191779
-
Genomic and transcriptional aberrations linked to breast cancer pathophysiologies
-
10.1016/j.ccr.2006.10.009 17157792
-
Chin K DeVries S Fridlyand J Spellman PT Roydasgupta R Kuo WL Lapuk A Neve RM Qian Z Ryder T Chen F Feiler H Tokuyasu T Kingsley C Dairkee S Meng Z Chew K Pinkel D Jain A Ljung BM Esserman L Albertson DG Waldman FM Gray JW Genomic and transcriptional aberrations linked to breast cancer pathophysiologies Cancer Cell 2006, 10:529-541. 10.1016/ j.ccr.2006.10.009 17157792
-
(2006)
Cancer Cell
, vol.10
, pp. 529-541
-
-
Chin, K.1
DeVries, S.2
Fridlyand, J.3
Spellman, P.T.4
Roydasgupta, R.5
Kuo, W.L.6
Lapuk, A.7
Neve, R.M.8
Qian, Z.9
Ryder, T.10
Chen, F.11
Feiler, H.12
Tokuyasu, T.13
Kingsley, C.14
Dairkee, S.15
Meng, Z.16
Chew, K.17
Pinkel, D.18
Jain, A.19
Ljung, B.M.20
Esserman, L.21
Albertson, D.G.22
Waldman, F.M.23
Gray, J.W.24
more..
-
32
-
-
10044254753
-
E2Fs link the control of G1/S and G2/M transcription
-
533046 15510213 10.1038/sj.emboj.7600459
-
Zhu W Giangrande PH Nevins JR E2Fs link the control of G1/S and G2/M transcription EMBO J 2004, 23:4615-4626. 533046 15510213 10.1038/ sj.emboj.7600459
-
(2004)
EMBO J
, vol.23
, pp. 4615-4626
-
-
Zhu, W.1
Giangrande, P.H.2
Nevins, J.R.3
-
33
-
-
0035515347
-
The ETS-domain transcription factor family
-
10.1038/35099076 11715049
-
Sharrocks AD The ETS-domain transcription factor family Nat Rev Mol Cell Biol 2001, 2:827-837. 10.1038/35099076 11715049
-
(2001)
Nat Rev Mol Cell Biol
, vol.2
, pp. 827-837
-
-
Sharrocks, A.D.1
-
34
-
-
18344372018
-
The RUNX genes: Gain or loss of function in cancer
-
10.1038/nrc1607 15864279
-
Blyth K Cameron ER Neil JC The RUNX genes: Gain or loss of function in cancer Nat Rev Cancer 2005, 5:376-387. 10.1038/nrc1607 15864279
-
(2005)
Nat Rev Cancer
, vol.5
, pp. 376-387
-
-
Blyth, K.1
Cameron, E.R.2
Neil, J.C.3
-
35
-
-
33845768987
-
Integrating cell-signalling pathways with NF-kappaB and IKK function
-
10.1038/nrm2083 17183360
-
Perkins ND Integrating cell-signalling pathways with NF-kappaB and IKK function Nat Rev Mol Cell Biol 2007, 8:49-62. 10.1038/nrm2083 17183360
-
(2007)
Nat Rev Mol Cell Biol
, vol.8
, pp. 49-62
-
-
Perkins, N.D.1
-
36
-
-
33748051738
-
IRFs: Master regulators of signalling by Toll-like receptors and cytosolic pattern-recognition receptors
-
10.1038/nri1900 16932750
-
Honda K Taniguchi T IRFs: Master regulators of signalling by Toll-like receptors and cytosolic pattern-recognition receptors Nat Rev Immunol 2006, 6:644-658. 10.1038/nri1900 16932750
-
(2006)
Nat Rev Immunol
, vol.6
, pp. 644-658
-
-
Honda, K.1
Taniguchi, T.2
-
37
-
-
34247625135
-
Pharmacologic disruption of Polycomb-repressive complex 2-mediated gene repression selectively induces apoptosis in cancer cells
-
1855231 17437993 10.1101/gad.1524107
-
Tan J Yang X Zhuang L Jiang X Chen W Lee PL Karuturi RK Tan PB Liu ET Yu Q Pharmacologic disruption of Polycomb-repressive complex 2-mediated gene repression selectively induces apoptosis in cancer cells Genes Dev 2007, 21:1050-1063. 1855231 17437993 10.1101/gad.1524107
-
(2007)
Genes Dev
, vol.21
, pp. 1050-1063
-
-
Tan, J.1
Yang, X.2
Zhuang, L.3
Jiang, X.4
Chen, W.5
Lee, P.L.6
Karuturi, R.K.7
Tan, P.B.8
Liu, E.T.9
Yu, Q.10
-
38
-
-
0142105414
-
EZH2 is downstream of the pRB-E2F pathway, essential for proliferation and amplified in cancer
-
213796 14532106 10.1093/emboj/cdg542
-
Bracken AP Pasini D Capra M Prosperini E Colli E Helin K EZH2 is downstream of the pRB-E2F pathway, essential for proliferation and amplified in cancer EMBO J 2003, 22:5323-5335. 213796 14532106 10.1093/ emboj/cdg542
-
(2003)
EMBO J
, vol.22
, pp. 5323-5335
-
-
Bracken, A.P.1
Pasini, D.2
Capra, M.3
Prosperini, E.4
Colli, E.5
Helin, K.6
-
39
-
-
42649112047
-
An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors
-
10.1038/ng.127 18443585
-
Ben-Porath I Thomson MW Carey VJ Ge R Bell GW Regev A Weinberg RA An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors Nature Genet 2008, 40:499-507. 10.1038/ng.127 18443585
-
(2008)
Nature Genet
, vol.40
, pp. 499-507
-
-
Ben-Porath, I.1
Thomson, M.W.2
Carey, V.J.3
Ge, R.4
Bell, G.W.5
Regev, A.6
Weinberg, R.A.7
-
40
-
-
22144486551
-
Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1
-
10.1016/j.cell.2005.05.008 16009131
-
Carroll JS Liu XS Brodsky AS Li W Meyer CA Szary AJ Eeckhoute J Shao W Hestermann EV Geistlinger TR Fox EA Silver PA Brown M Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1 Cell 2005, 122:33-43. 10.1016/ j.cell.2005.05.008 16009131
-
(2005)
Cell
, vol.122
, pp. 33-43
-
-
Carroll, J.S.1
Liu, X.S.2
Brodsky, A.S.3
Li, W.4
Meyer, C.A.5
Szary, A.J.6
Eeckhoute, J.7
Shao, W.8
Hestermann, E.V.9
Geistlinger, T.R.10
Fox, E.A.11
Silver, P.A.12
Brown, M.13
-
41
-
-
33749148764
-
Modularity of the transcriptional response of protein complexes in yeast
-
10.1016/j.jmb.2006.06.024 16973176
-
Simonis N Gonze D Orsi C van Helden J Wodak SJ Modularity of the transcriptional response of protein complexes in yeast J Mol Biol 2006, 363:589-610. 10.1016/j.jmb.2006.06.024 16973176
-
(2006)
J Mol Biol
, vol.363
, pp. 589-610
-
-
Simonis, N.1
Gonze, D.2
Orsi, C.3
van Helden, J.4
Wodak, S.J.5
-
42
-
-
0141792394
-
Correlating protein-DNA and protein-protein interaction networks
-
10.1016/j.jmb.2003.08.004 14516744
-
Manke T Bringas R Vingron M Correlating protein-DNA and protein-protein interaction networks J Mol Biol 2003, 333:75-85. 10.1016/ j.jmb.2003.08.004 14516744
-
(2003)
J Mol Biol
, vol.333
, pp. 75-85
-
-
Manke, T.1
Bringas, R.2
Vingron, M.3
-
43
-
-
3042822267
-
Cancer and the chemokine network
-
10.1038/nrc1388 15229479
-
Balkwill F Cancer and the chemokine network Nat Rev Cancer 2004, 4:540-550. 10.1038/nrc1388 15229479
-
(2004)
Nat Rev Cancer
, vol.4
, pp. 540-550
-
-
Balkwill, F.1
-
44
-
-
34948896045
-
Mesenchymal stem cells within tumour stroma promote breast cancer metastasis
-
10.1038/nature06188 17914389
-
Karnoub AE Dash AB Vo AP Sullivan A Brooks MW Bell GW Richardson AL Polyak K Tubo R Weinberg RA Mesenchymal stem cells within tumour stroma promote breast cancer metastasis Nature 2007, 449:557-563. 10.1038/ nature06188 17914389
-
(2007)
Nature
, vol.449
, pp. 557-563
-
-
Karnoub, A.E.1
Dash, A.B.2
Vo, A.P.3
Sullivan, A.4
Brooks, M.W.5
Bell, G.W.6
Richardson, A.L.7
Polyak, K.8
Tubo, R.9
Weinberg, R.A.10
-
45
-
-
33745847481
-
Interferon regulatory factor 8 regulates RANTES gene transcription in cooperation with interferon regulatory factor-1, NF-kappaB, and PU.1
-
10.1074/jbc.M602059200 16707500
-
Liu J Ma X Interferon regulatory factor 8 regulates RANTES gene transcription in cooperation with interferon regulatory factor-1, NF-kappaB, and PU.1 J Biol Chem 2006, 281:19188-19195. 10.1074/ jbc.M602059200 16707500
-
(2006)
J Biol Chem
, vol.281
, pp. 19188-19195
-
-
Liu, J.1
Ma, X.2
-
46
-
-
3142512612
-
Molecular characterization of the tumor microenvironment in breast cancer
-
10.1016/j.ccr.2004.06.010 15261139
-
Allinen M Beroukhim R Cai L Brennan C Lahti-Domenici J Huang H Porter D Hu M Chin L Richardson A Schnitt S Sellers WR Polyak K Molecular characterization of the tumor microenvironment in breast cancer Cancer Cell 2004, 6:17-32. 10.1016/j.ccr.2004.06.010 15261139
-
(2004)
Cancer Cell
, vol.6
, pp. 17-32
-
-
Allinen, M.1
Beroukhim, R.2
Cai, L.3
Brennan, C.4
Lahti-Domenici, J.5
Huang, H.6
Porter, D.7
Hu, M.8
Chin, L.9
Richardson, A.10
Schnitt, S.11
Sellers, W.R.12
Polyak, K.13
-
47
-
-
6944244084
-
A module map showing conditional activity of expression modules in cancer
-
10.1038/ng1434 15448693
-
Segal E Friedman N Koller D Regev A A module map showing conditional activity of expression modules in cancer Nat Genet 2004, 36:1090-1098. 10.1038/ng1434 15448693
-
(2004)
Nat Genet
, vol.36
, pp. 1090-1098
-
-
Segal, E.1
Friedman, N.2
Koller, D.3
Regev, A.4
-
48
-
-
31144459985
-
Oncogenic pathway signatures in human cancers as a guide to targeted therapies
-
10.1038/nature04296 16273092
-
Bild AH Yao G Chang JT Wang Q Potti A Chasse D Joshi MB Harpole D Lancaster JM Berchuck A Olson JA Jr Marks JR Dressman HK West M Nevins JR Oncogenic pathway signatures in human cancers as a guide to targeted therapies Nature 2006, 439:353-357. 10.1038/nature04296 16273092
-
(2006)
Nature
, vol.439
, pp. 353-357
-
-
Bild, A.H.1
Yao, G.2
Chang, J.T.3
Wang, Q.4
Potti, A.5
Chasse, D.6
Joshi, M.B.7
Harpole, D.8
Lancaster, J.M.9
Berchuck, A.10
Olson Jr., J.A.11
Marks, J.R.12
Dressman, H.K.13
West, M.14
Nevins, J.R.15
-
50
-
-
38749102349
-
Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis
-
2217565 18021416 10.1186/1471-2105-8-453
-
Kim TM Chung YJ Rhyu MG Jung MH Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis BMC Bioinformatics 2007, 8:453. 2217565 18021416 10.1186/1471-2105-8-453
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 453
-
-
Kim, T.M.1
Chung, Y.J.2
Rhyu, M.G.3
Jung, M.H.4
-
51
-
-
9644268153
-
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays
-
10.1038/ng1473 15543148
-
Mukherjee S Berger MF Jona G Wang XS Muzzey D Snyder M Young RA Bulyk ML Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays Nat Genet 2004, 36:1331-1339. 10.1038/ng1473 15543148
-
(2004)
Nat Genet
, vol.36
, pp. 1331-1339
-
-
Mukherjee, S.1
Berger, M.F.2
Jona, G.3
Wang, X.S.4
Muzzey, D.5
Snyder, M.6
Young, R.A.7
Bulyk, M.L.8
-
52
-
-
33750882505
-
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
-
10.1038/nbt1246 16998473
-
Berger MF Philippakis AA Qureshi AM He FS Estep PW 3rd Bulyk ML Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities Nat Biotechnol 2006, 24:1429-1435. 10.1038/nbt1246 16998473
-
(2006)
Nat Biotechnol
, vol.24
, pp. 1429-1435
-
-
Berger, M.F.1
Philippakis, A.A.2
Qureshi, A.M.3
He, F.S.4
Estep III, P.W.5
Bulyk, M.L.6
-
53
-
-
34249026300
-
High-resolution profiling of histone methylations in the human genome
-
10.1016/j.cell.2007.05.009 17512414
-
Barski A Cuddapah S Cui K Roh TY Schones DE Wang Z Wei G Chepelev I Zhao K High-resolution profiling of histone methylations in the human genome Cell 2007, 129:823-837. 10.1016/j.cell.2007.05.009 17512414
-
(2007)
Cell
, vol.129
, pp. 823-837
-
-
Barski, A.1
Cuddapah, S.2
Cui, K.3
Roh, T.Y.4
Schones, D.E.5
Wang, Z.6
Wei, G.7
Chepelev, I.8
Zhao, K.9
-
54
-
-
34250159524
-
Genome-wide mapping of in vivo protein-DNA interactions
-
10.1126/science.1141319 17540862
-
Johnson DS Mortazavi A Myers RM Wold B Genome-wide mapping of in vivo protein-DNA interactions Science 2007, 316:1497-1502. 10.1126/ science.1141319 17540862
-
(2007)
Science
, vol.316
, pp. 1497-1502
-
-
Johnson, D.S.1
Mortazavi, A.2
Myers, R.M.3
Wold, B.4
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