-
1
-
-
27344435774
-
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
-
10.1073/pnas.0506580102, 1239896, 16199517
-
Subramanian A, Tamayo P, VK M, Mukherjee S, Ebert B, Gillette M, Paulovich A, Pomeroy S, Golub T, Lander E, Mesirov J. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 2005, 102:15545-15550. 10.1073/pnas.0506580102, 1239896, 16199517.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
VK, M.3
Mukherjee, S.4
Ebert, B.5
Gillette, M.6
Paulovich, A.7
Pomeroy, S.8
Golub, T.9
Lander, E.10
Mesirov, J.11
-
2
-
-
33847324900
-
Extensions to gene set enrichment
-
10.1093/bioinformatics/btl599, 17127676
-
Jiang Z, Gentleman R. Extensions to gene set enrichment. Bioinformatics 2007, 23:306-313. 10.1093/bioinformatics/btl599, 17127676.
-
(2007)
Bioinformatics
, vol.23
, pp. 306-313
-
-
Jiang, Z.1
Gentleman, R.2
-
3
-
-
70349753297
-
Comparative study of gene set enrichment methods
-
Abatangelo L, Maglietta R, Distaso A, D'Addabbo A, Creanza T, Mukherjee S, Ancona N. Comparative study of gene set enrichment methods. BMC Bioinf 2009, 10:275.
-
(2009)
BMC Bioinf
, vol.10
, pp. 275
-
-
Abatangelo, L.1
Maglietta, R.2
Distaso, A.3
D'Addabbo, A.4
Creanza, T.5
Mukherjee, S.6
Ancona, N.7
-
4
-
-
0742304254
-
Prediction of protein function using protein-protein interaction data
-
10.1089/106652703322756168, 14980019
-
Deng M, Zhang K, Mehta S, Chen T, Sun F. Prediction of protein function using protein-protein interaction data. J Comput Biol 2003, 10:947-960. 10.1089/106652703322756168, 14980019.
-
(2003)
J Comput Biol
, vol.10
, pp. 947-960
-
-
Deng, M.1
Zhang, K.2
Mehta, S.3
Chen, T.4
Sun, F.5
-
5
-
-
75949120438
-
How and when should interactome-derived clusters be used to predict functional modules and protein function?
-
10.1093/bioinformatics/btp551, 3167697, 19770263
-
Song J, Singh M. How and when should interactome-derived clusters be used to predict functional modules and protein function?. Bioinformatics 2009, 25:3143-3150. 10.1093/bioinformatics/btp551, 3167697, 19770263.
-
(2009)
Bioinformatics
, vol.25
, pp. 3143-3150
-
-
Song, J.1
Singh, M.2
-
6
-
-
77950672712
-
Network-based identification of novel cancer genes
-
10.1074/mcp.M900227-MCP200, 2860235, 19959820
-
Ostlund G, Lindskog M, Sonnhammer E. Network-based identification of novel cancer genes. Mol Cell Proteomics 2010, 9:648-655. 10.1074/mcp.M900227-MCP200, 2860235, 19959820.
-
(2010)
Mol Cell Proteomics
, vol.9
, pp. 648-655
-
-
Ostlund, G.1
Lindskog, M.2
Sonnhammer, E.3
-
7
-
-
78049236574
-
Genome-wide pathway analysis implicates intracellular transmembrane protein transport in Alzheimer disease
-
Hong M, Alexeyenko A, Lambert J, Amouyel P, Prince J. Genome-wide pathway analysis implicates intracellular transmembrane protein transport in Alzheimer disease. J Human Genet 2010, 55:707-709.
-
(2010)
J Human Genet
, vol.55
, pp. 707-709
-
-
Hong, M.1
Alexeyenko, A.2
Lambert, J.3
Amouyel, P.4
Prince, J.5
-
8
-
-
66449120271
-
Exploring the human genome with functional maps
-
10.1101/gr.082214.108, 2694471, 19246570
-
Huttenhower C, Haley E, Hibbs M, Dumeaux V, Barrett D, Coller H, Troyanskaya O. Exploring the human genome with functional maps. Genome Res 2009, 19:1093-1106. 10.1101/gr.082214.108, 2694471, 19246570.
-
(2009)
Genome Res
, vol.19
, pp. 1093-1106
-
-
Huttenhower, C.1
Haley, E.2
Hibbs, M.3
Dumeaux, V.4
Barrett, D.5
Coller, H.6
Troyanskaya, O.7
-
9
-
-
77953084703
-
Network enrichment analysis in complex experiments
-
2898649, 20597848
-
Shojaie A, Michailidis G. Network enrichment analysis in complex experiments. Stat Appl Genet Mol Biol 2010, 9(1):Article22. 2898649, 20597848.
-
(2010)
Stat Appl Genet Mol Biol
, vol.9
, Issue.1
-
-
Shojaie, A.1
Michailidis, G.2
-
10
-
-
0000801240
-
Discovering regulatory and signalling circuits in molecular interaction networks
-
Ideker T, Ozier O, Schwikowski B, Siegel A. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 2002, 18(Suppl 1):S233-S240.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Ideker, T.1
Ozier, O.2
Schwikowski, B.3
Siegel, A.4
-
11
-
-
0242490780
-
Cytoscape: a software environment for integrated models of biomolecular interaction networks
-
10.1101/gr.1239303, 403769, 14597658
-
Shannon P, Markiel A, Ozier O, Baliga N, Wang J, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13(11):2498-2504. 10.1101/gr.1239303, 403769, 14597658.
-
(2003)
Genome Res
, vol.13
, Issue.11
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.4
Wang, J.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
-
12
-
-
34347326247
-
Network-based analysis of affected biological processes in type 2 diabetes models
-
10.1371/journal.pgen.0030096, 1904360, 17571924
-
Liu M, Liberzon A, Kong S, Lai W, Park P, Kohane I, Kasif S. Network-based analysis of affected biological processes in type 2 diabetes models. PLoS Genet 2007, 3(6):e96. 10.1371/journal.pgen.0030096, 1904360, 17571924.
-
(2007)
PLoS Genet
, vol.3
, Issue.6
-
-
Liu, M.1
Liberzon, A.2
Kong, S.3
Lai, W.4
Park, P.5
Kohane, I.6
Kasif, S.7
-
13
-
-
74049140006
-
Early pregnancy peripheral blood gene expression and risk of preterm delivery: a nested case control study
-
10.1186/1471-2393-9-56, 2799378, 20003277
-
Enquobahrie D, Williams M, Qiu C, Muhie S, Slentz-Kesler K, Ge Z, Sorenson T. Early pregnancy peripheral blood gene expression and risk of preterm delivery: a nested case control study. BMC Pregnancy Childbirth 2009, 9:56. 10.1186/1471-2393-9-56, 2799378, 20003277.
-
(2009)
BMC Pregnancy Childbirth
, vol.9
, pp. 56
-
-
Enquobahrie, D.1
Williams, M.2
Qiu, C.3
Muhie, S.4
Slentz-Kesler, K.5
Ge, Z.6
Sorenson, T.7
-
14
-
-
77955463831
-
Exon-level microarray analyses identify alternative splicing programs in breast cancer
-
10.1158/1541-7786.MCR-09-0528, 2911965, 20605923
-
Lapuk A, Marr H, Jakkula L, Pedro H, Bhattacharya S, Purdom E, Hu Z, Simpson K, Pachter L, Durinck S, Wang N, Parvin B, Fontenay G, Speed T, Garbe J, Stampfer M, Bayandorian H, Dorton S, Clark T, Schweitzer A, Wyrobek A, Feiler H, Spellman P, Conboy J, Gray J. Exon-level microarray analyses identify alternative splicing programs in breast cancer. Mol Cancer Res 2010, 8:961-974. 10.1158/1541-7786.MCR-09-0528, 2911965, 20605923.
-
(2010)
Mol Cancer Res
, vol.8
, pp. 961-974
-
-
Lapuk, A.1
Marr, H.2
Jakkula, L.3
Pedro, H.4
Bhattacharya, S.5
Purdom, E.6
Hu, Z.7
Simpson, K.8
Pachter, L.9
Durinck, S.10
Wang, N.11
Parvin, B.12
Fontenay, G.13
Speed, T.14
Garbe, J.15
Stampfer, M.16
Bayandorian, H.17
Dorton, S.18
Clark, T.19
Schweitzer, A.20
Wyrobek, A.21
Feiler, H.22
Spellman, P.23
Conboy, J.24
Gray, J.25
more..
-
15
-
-
31144459985
-
Oncogenic pathway signatures in human cancers as a guide to targeted theraphies
-
10.1038/nature04296, 16273092
-
Bild A, Yao G, Change J, Qang Q, Potti A, Chasse D, Joshi M, Harpole D, Lancaster J, Berchuck A, Olson J, Marks J, Dressman H, West M, Nevins J. Oncogenic pathway signatures in human cancers as a guide to targeted theraphies. Nature 2006, 439:353-357. 10.1038/nature04296, 16273092.
-
(2006)
Nature
, vol.439
, pp. 353-357
-
-
Bild, A.1
Yao, G.2
Change, J.3
Qang, Q.4
Potti, A.5
Chasse, D.6
Joshi, M.7
Harpole, D.8
Lancaster, J.9
Berchuck, A.10
Olson, J.11
Marks, J.12
Dressman, H.13
West, M.14
Nevins, J.15
-
16
-
-
4544341015
-
Linear models and empirical bayes methods for assessing differential expression in microarray experiments
-
Smyth G. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004, 3(1):Article3.
-
(2004)
Stat Appl Genet Mol Biol
, vol.3
, Issue.1
-
-
Smyth, G.1
-
17
-
-
77956508108
-
Dynamic zebrafish interactome reveals transcriptional mechanisms of dioxin toxicity
-
Meyer J
-
Alexeyenko A, Wassenberg D, Lobenhofer E, Yen J, Linney E, Sonnhammer E, . Meyer J Dynamic zebrafish interactome reveals transcriptional mechanisms of dioxin toxicity. PloS One 2010, 5(5):e:10465. Meyer J.
-
(2010)
PloS One
, vol.5
, Issue.5
-
-
Alexeyenko, A.1
Wassenberg, D.2
Lobenhofer, E.3
Yen, J.4
Linney, E.5
Sonnhammer, E.6
-
18
-
-
45449101889
-
A global pathway crosstalk network
-
10.1093/bioinformatics/btn200, 18434343
-
Li Y, Agarwal P, Rajagopalan D. A global pathway crosstalk network. Bioinformatics 2008, 24:1442-1447. 10.1093/bioinformatics/btn200, 18434343.
-
(2008)
Bioinformatics
, vol.24
, pp. 1442-1447
-
-
Li, Y.1
Agarwal, P.2
Rajagopalan, D.3
-
19
-
-
0035420732
-
Random graphs with arbitrary degree distributions and their applications
-
Newman M, Strogatz S, Watts D. Random graphs with arbitrary degree distributions and their applications. Phys Rev E 2001, 64:026118.
-
(2001)
Phys Rev E
, vol.64
, pp. 026118
-
-
Newman, M.1
Strogatz, S.2
Watts, D.3
-
20
-
-
0037012880
-
Specificity and stability in topology of protein networks
-
10.1126/science.1065103, 11988575
-
Maslov S, Sneppen K. Specificity and stability in topology of protein networks. Science 2002, 296:910-913. 10.1126/science.1065103, 11988575.
-
(2002)
Science
, vol.296
, pp. 910-913
-
-
Maslov, S.1
Sneppen, K.2
-
21
-
-
65349085291
-
Global networks of functional coupling in eukaryotes from comprehensive data integration
-
10.1101/gr.087528.108, 2694487, 19246318
-
Alexeyenko A, Sonnhammer E. Global networks of functional coupling in eukaryotes from comprehensive data integration. Genome Res 2009, 19:1107-1116. 10.1101/gr.087528.108, 2694487, 19246318.
-
(2009)
Genome Res
, vol.19
, pp. 1107-1116
-
-
Alexeyenko, A.1
Sonnhammer, E.2
-
22
-
-
77949446630
-
Automated network analysis identifies core pathways in glioblastoma
-
10.1371/journal.pone.0008918, 2820542, 20169195
-
Cerami E, Demir E, Schultz N, Taylor B, Sander C. Automated network analysis identifies core pathways in glioblastoma. PLoS One 2010, 5(2):e8918. 10.1371/journal.pone.0008918, 2820542, 20169195.
-
(2010)
PLoS One
, vol.5
, Issue.2
-
-
Cerami, E.1
Demir, E.2
Schultz, N.3
Taylor, B.4
Sander, C.5
-
23
-
-
14944358428
-
Sequential monte carlo methods for statistical analysis of tables
-
Chen Y, Holmes S, Liu J. Sequential monte carlo methods for statistical analysis of tables. J Am Stat Assoc 2005, 100:109-120.
-
(2005)
J Am Stat Assoc
, vol.100
, pp. 109-120
-
-
Chen, Y.1
Holmes, S.2
Liu, J.3
-
24
-
-
27544510142
-
False discovery rate, sensitivity and sample size for microarray studies
-
10.1093/bioinformatics/bti626, 16105901
-
Pawitan Y, Michiels S, Koscielny S, Gusnanto A, Ploner A. False discovery rate, sensitivity and sample size for microarray studies. Bioinformatics 2005, 21:3865-3872. 10.1093/bioinformatics/bti626, 16105901.
-
(2005)
Bioinformatics
, vol.21
, pp. 3865-3872
-
-
Pawitan, Y.1
Michiels, S.2
Koscielny, S.3
Gusnanto, A.4
Ploner, A.5
-
25
-
-
79952284127
-
Hallmarks of cancer: the next generation
-
10.1016/j.cell.2011.02.013, 21376230
-
Hanahan D, Weinberg R. Hallmarks of cancer: the next generation. Cell 2011, 144:646-674. 10.1016/j.cell.2011.02.013, 21376230.
-
(2011)
Cell
, vol.144
, pp. 646-674
-
-
Hanahan, D.1
Weinberg, R.2
-
26
-
-
54549094903
-
Somantic mutations affect key pathways in lung adenocarcinoma
-
10.1038/nature07423, 2694412, 18948947
-
Ding L, Getz G, Wheeler D, Mardis E, McLellan M, Cibulskis K, Sougnez C, Greulich H, Muzny D, Morgan M, Fulton L, Fulton R, Zhang Q, Wendl M, Lawrence M, Larson D, Chen K, Dooling D, Sabo A, Hawes A, Shen H, Jhangiani S, Lewis L, Hall O, Zhu Y, Mathew T, Ren Y, Yao J, Scherer S, Clerc K, et al. Somantic mutations affect key pathways in lung adenocarcinoma. Nature 2008, 455:1069-1075. 10.1038/nature07423, 2694412, 18948947.
-
(2008)
Nature
, vol.455
, pp. 1069-1075
-
-
Ding, L.1
Getz, G.2
Wheeler, D.3
Mardis, E.4
McLellan, M.5
Cibulskis, K.6
Sougnez, C.7
Greulich, H.8
Muzny, D.9
Morgan, M.10
Fulton, L.11
Fulton, R.12
Zhang, Q.13
Wendl, M.14
Lawrence, M.15
Larson, D.16
Chen, K.17
Dooling, D.18
Sabo, A.19
Hawes, A.20
Shen, H.21
Jhangiani, S.22
Lewis, L.23
Hall, O.24
Zhu, Y.25
Mathew, T.26
Ren, Y.27
Yao, J.28
Scherer, S.29
Clerc, K.30
more..
-
27
-
-
75549087826
-
COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer
-
2808858, 19906727
-
Forbes S, Tang G, Bindal N, Bamford S, Dawson E, Cole C, Kok C, Jia M, Ewing R, Menzies A, Teague J, MR S, Futreal P. COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer. Nucl Acids Res 2010, 38:D652-D657. 2808858, 19906727.
-
(2010)
Nucl Acids Res
, vol.38
-
-
Forbes, S.1
Tang, G.2
Bindal, N.3
Bamford, S.4
Dawson, E.5
Cole, C.6
Kok, C.7
Jia, M.8
Ewing, R.9
Menzies, A.10
Teague, J.11
MR, S.12
Futreal, P.13
-
29
-
-
77954376945
-
GOing Bayesian: model-based gene set analysis of genome-scale data
-
10.1093/nar/gkq045, 2887944, 20172960
-
Bauer S, Gagneur J, Robinson P. GOing Bayesian: model-based gene set analysis of genome-scale data. Nucleic Acids Res 2010, 38(11):3523-3532. 10.1093/nar/gkq045, 2887944, 20172960.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.11
, pp. 3523-3532
-
-
Bauer, S.1
Gagneur, J.2
Robinson, P.3
-
30
-
-
33745626459
-
Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
-
10.1093/bioinformatics/btl140, 16606683
-
Alexa A, Rahnenfuhrer J, Lengauer T. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 2006, 22(13):1600-1607. 10.1093/bioinformatics/btl140, 16606683.
-
(2006)
Bioinformatics
, vol.22
, Issue.13
, pp. 1600-1607
-
-
Alexa, A.1
Rahnenfuhrer, J.2
Lengauer, T.3
-
31
-
-
78651324347
-
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
-
[doi:10.1093/nar/gkq973], 10.1093/nar/gkq973, 3013807, 21045058
-
Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen L, von Mering C. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 2011, 39:D561-8. [doi:10.1093/nar/gkq973], 10.1093/nar/gkq973, 3013807, 21045058.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Szklarczyk, D.1
Franceschini, A.2
Kuhn, M.3
Simonovic, M.4
Roth, A.5
Minguez, P.6
Doerks, T.7
Stark, M.8
Muller, J.9
Bork, P.10
Jensen, L.11
von Mering, C.12
-
32
-
-
18744389789
-
Assortative mixing in networks
-
Newman M. Assortative mixing in networks. Phys Rev Lett 2002, 89:28701.
-
(2002)
Phys Rev Lett
, vol.89
, pp. 28701
-
-
Newman, M.1
|