-
1
-
-
33748597382
-
Network theory to understand microarray studies of complex diseases
-
Benson, M. & Breitling, R. Network theory to understand microarray studies of complex diseases. Curr. Mol. Med. 6, 695-701 (2006).
-
(2006)
Curr. Mol. Med
, vol.6
, pp. 695-701
-
-
Benson, M.1
Breitling, R.2
-
2
-
-
0346156102
-
Detection of functional modules from protein interaction networks
-
Pereira-Leal, J.B., Enright, A.J. & Ouzounis, C.A. Detection of functional modules from protein interaction networks. Proteins 54, 49-57 (2004).
-
(2004)
Proteins
, vol.54
, pp. 49-57
-
-
Pereira-Leal, J.B.1
Enright, A.J.2
Ouzounis, C.A.3
-
3
-
-
0037168519
-
A systematic approach to reconstructing transcription networks in Saccharomyces cerevisiae
-
Wang, W., Cherry, J.M., Botstein, D. & Li, H. A systematic approach to reconstructing transcription networks in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 99, 16893-16898 (2002).
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 16893-16898
-
-
Wang, W.1
Cherry, J.M.2
Botstein, D.3
Li, H.4
-
4
-
-
33846057516
-
Regulatory networks: Linking microarray data to systems biology
-
Werner, T. Regulatory networks: linking microarray data to systems biology. Mech. Ageing Dev. 128, 168-172 (2007).
-
(2007)
Mech. Ageing Dev
, vol.128
, pp. 168-172
-
-
Werner, T.1
-
5
-
-
0034730140
-
Singular value decomposition for genomewide expression data processing and modeling
-
Alter, O., Brown, P.O. & Botstein, D. Singular value decomposition for genomewide expression data processing and modeling. Proc. Natl. Acad. Sci. USA 97, 10101-10106 (2000).
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 10101-10106
-
-
Alter, O.1
Brown, P.O.2
Botstein, D.3
-
6
-
-
0037057374
-
Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering
-
RESEARCH0059
-
Gasch, A.P. & Eisen, M.B. Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biol. 3, RESEARCH0059 (2002).
-
(2002)
Genome Biol
, vol.3
-
-
Gasch, A.P.1
Eisen, M.B.2
-
7
-
-
0038109937
-
Coupled two-way clustering analysis of breast cancer and colon cancer gene expression data
-
Getz, G., Gal, H., Kela, I., Notterman, D.A. & Domany, E. Coupled two-way clustering analysis of breast cancer and colon cancer gene expression data. Bioinformatics 19, 1079-1089 (2003).
-
(2003)
Bioinformatics
, vol.19
, pp. 1079-1089
-
-
Getz, G.1
Gal, H.2
Kela, I.3
Notterman, D.A.4
Domany, E.5
-
8
-
-
0034682504
-
Fundamental patterns underlying gene expression profiles: Simplicity from complexity
-
Holter, N.S. et al. Fundamental patterns underlying gene expression profiles: simplicity from complexity. Proc. Natl. Acad. Sci. USA 97, 8409-8414 (2000).
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 8409-8414
-
-
Holter, N.S.1
-
9
-
-
0036699526
-
Revealing modular organization in the yeast transcriptional network
-
Ihmels, J. et al. Revealing modular organization in the yeast transcriptional network. Nat. Genet. 31, 370-377 (2002).
-
(2002)
Nat. Genet
, vol.31
, pp. 370-377
-
-
Ihmels, J.1
-
10
-
-
2442446708
-
Genome-wide discovery of transcriptional modules from DNA sequence and gene expression
-
Segal, E., Yelensky, R. & Koller, D. Genome-wide discovery of transcriptional modules from DNA sequence and gene expression. Bioinformatics 19 Suppl 1, i273-i282 (2003).
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 1
-
-
Segal, E.1
Yelensky, R.2
Koller, D.3
-
11
-
-
1542357674
-
Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data
-
Tanay, A., Sharan, R., Kupiec, M. & Shamir, R. Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data. Proc. Natl. Acad. Sci. USA 101, 2981-2986 (2004).
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 2981-2986
-
-
Tanay, A.1
Sharan, R.2
Kupiec, M.3
Shamir, R.4
-
12
-
-
0031035181
-
An information-intensive approach to the molecular pharmacology of cancer
-
Weinstein, J.N. et al. An information-intensive approach to the molecular pharmacology of cancer. Science 275, 343-349 (1997).
-
(1997)
Science
, vol.275
, pp. 343-349
-
-
Weinstein, J.N.1
-
13
-
-
0035845531
-
Chemosensitivity prediction by transcriptional profiling
-
Staunton, J.E. et al. Chemosensitivity prediction by transcriptional profiling. Proc. Natl. Acad. Sci. USA 98, 10787-10792 (2001).
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 10787-10792
-
-
Staunton, J.E.1
-
14
-
-
34147115178
-
Transcript and protein expression profiles of the NCI-60 cancer cell panel: An integromic microarray study
-
Shankavaram, U.T. et al. Transcript and protein expression profiles of the NCI-60 cancer cell panel: an integromic microarray study. Mol. Cancer Ther. 6, 820-832 (2007).
-
(2007)
Mol. Cancer Ther
, vol.6
, pp. 820-832
-
-
Shankavaram, U.T.1
-
15
-
-
34047270440
-
Characterization of microRNA expression levels and their biological correlates in human cancer cell lines
-
Gaur, A. et al. Characterization of microRNA expression levels and their biological correlates in human cancer cell lines. Cancer Res. 67, 2456-2468 (2007).
-
(2007)
Cancer Res
, vol.67
, pp. 2456-2468
-
-
Gaur, A.1
-
16
-
-
33646541046
-
Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel
-
Bussey, K.J. et al. Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel. Mol. Cancer Ther. 5, 853-867 (2006).
-
(2006)
Mol. Cancer Ther
, vol.5
, pp. 853-867
-
-
Bussey, K.J.1
-
17
-
-
0034088857
-
A gene expression database for the molecular pharmacology of cancer
-
Scherf, U. et al. A gene expression database for the molecular pharmacology of cancer. Nat. Genet. 24, 236-244 (2000).
-
(2000)
Nat. Genet
, vol.24
, pp. 236-244
-
-
Scherf, U.1
-
18
-
-
84864994884
-
Iterative signature algorithm for the analysis of large-scale gene expression data
-
Bergmann, S., Ihmels, J. & Barkai, N. Iterative signature algorithm for the analysis of large-scale gene expression data. Phys. Rev. E 67, 031902 (2003).
-
(2003)
Phys. Rev. E
, vol.67
, pp. 031902
-
-
Bergmann, S.1
Ihmels, J.2
Barkai, N.3
-
19
-
-
33751327438
-
Comparative gene expression analysis by differential clustering approach: Application to the Candida albicans transcription program
-
Ihmels, J., Bergmann, S., Berman, J. & Barkai, N. Comparative gene expression analysis by differential clustering approach: application to the Candida albicans transcription program. PLoS Genet. 1, e39 (2005).
-
(2005)
PLoS Genet
, vol.1
-
-
Ihmels, J.1
Bergmann, S.2
Berman, J.3
Barkai, N.4
-
20
-
-
33646137384
-
A systematic comparison and evaluation of biclustering methods for gene expression data
-
Prelic, A. et al. A systematic comparison and evaluation of biclustering methods for gene expression data. Bioinformatics 22, 1122-1129 (2006).
-
(2006)
Bioinformatics
, vol.22
, pp. 1122-1129
-
-
Prelic, A.1
-
21
-
-
4544339167
-
Defining transcription modules using large-scale gene expression data
-
Ihmels, J., Bergmann, S. & Barkai, N. Defining transcription modules using large-scale gene expression data. Bioinformatics 20, 1993-2003 (2004).
-
(2004)
Bioinformatics
, vol.20
, pp. 1993-2003
-
-
Ihmels, J.1
Bergmann, S.2
Barkai, N.3
-
22
-
-
19344374050
-
Similarities and differences in genome-wide expression data of six organisms
-
Bergmann, S., Ihmels, J. & Barkai, N. Similarities and differences in genome-wide expression data of six organisms. PLoS Biol. 2, E9 (2004).
-
(2004)
PLoS Biol
, vol.2
-
-
Bergmann, S.1
Ihmels, J.2
Barkai, N.3
-
23
-
-
23244467882
-
Rewiring of the yeast transcriptional network through the evolution of motif usage
-
Ihmels, J. et al. Rewiring of the yeast transcriptional network through the evolution of motif usage. Science 309, 938-940 (2005).
-
(2005)
Science
, vol.309
, pp. 938-940
-
-
Ihmels, J.1
-
24
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25-29 (2000).
-
(2000)
Nat. Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
-
25
-
-
0024312538
-
Display and analysis of patterns of differential activity of drugs against human tumor cell lines: Development of mean graph and COMPARE algorithm
-
Paull, K.D. et al. Display and analysis of patterns of differential activity of drugs against human tumor cell lines: development of mean graph and COMPARE algorithm. J. Natl. Cancer Inst. 81, 1088-1092 (1989).
-
(1989)
J. Natl. Cancer Inst
, vol.81
, pp. 1088-1092
-
-
Paull, K.D.1
-
26
-
-
33748060533
-
Predicting cancer drug response by proteomic profiling
-
Ma, Y. et al. Predicting cancer drug response by proteomic profiling. Clin. Cancer Res. 12, 4583-4589 (2006).
-
(2006)
Clin. Cancer Res
, vol.12
, pp. 4583-4589
-
-
Ma, Y.1
-
27
-
-
2942582468
-
Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data
-
Gao, F., Foat, B.C. & Bussemaker, H.J. Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. BMC Bioinformatics 5, 31 (2004).
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 31
-
-
Gao, F.1
Foat, B.C.2
Bussemaker, H.J.3
-
28
-
-
34848855728
-
Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data
-
Liu, X., Jessen, W.J., Sivaganesan, S., Aronow, B.J. & Medvedovic, M. Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data. BMC Bioinformatics 8, 283 (2007).
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 283
-
-
Liu, X.1
Jessen, W.J.2
Sivaganesan, S.3
Aronow, B.J.4
Medvedovic, M.5
-
29
-
-
6944244084
-
A module map showing conditional activity of expression modules in cancer
-
Segal, E., Friedman, N., Koller, D. & Regev, A. A module map showing conditional activity of expression modules in cancer. Nat. Genet. 36, 1090-1098 (2004).
-
(2004)
Nat. Genet
, vol.36
, pp. 1090-1098
-
-
Segal, E.1
Friedman, N.2
Koller, D.3
Regev, A.4
-
30
-
-
0037941585
-
Module networks: Identifying regulatory modules and their conditionspecific regulators from gene expression data
-
Segal, E. et al. Module networks: identifying regulatory modules and their conditionspecific regulators from gene expression data. Nat. Genet. 34, 166-176 (2003).
-
(2003)
Nat. Genet
, vol.34
, pp. 166-176
-
-
Segal, E.1
-
31
-
-
33644876210
-
DrugBank: A comprehensive resource for in silico drug discovery and exploration
-
Wishart, D.S. et al. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 34, D668-D672 (2006).
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Wishart, D.S.1
-
32
-
-
33749335282
-
The Connectivity Map: Using gene-expression signatures to connect small molecules, genes, and disease
-
Lamb, J. et al. The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science 313, 1929-1935 (2006).
-
(2006)
Science
, vol.313
, pp. 1929-1935
-
-
Lamb, J.1
-
33
-
-
0027457620
-
Receiver-operating characteristic (ROC) plots: A fundamental evaluation tool in clinical medicine
-
Zweig, M.H. & Campbell, G. Receiver-operating characteristic (ROC) plots: a fundamental evaluation tool in clinical medicine. Clin. Chem. 39, 561-577 (1993).
-
(1993)
Clin. Chem
, vol.39
, pp. 561-577
-
-
Zweig, M.H.1
Campbell, G.2
-
34
-
-
33644874819
-
From genomics to chemical genomics: New developments in KEGG
-
Kanehisa, M. et al. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34, D354-D357 (2006).
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Kanehisa, M.1
-
35
-
-
31444435675
-
Characterization of the activities of actin-affecting drugs on tumor cell migration
-
Hayot, C. et al. Characterization of the activities of actin-affecting drugs on tumor cell migration. Toxicol. Appl. Pharmacol. 211, 30-40 (2006).
-
(2006)
Toxicol. Appl. Pharmacol
, vol.211
, pp. 30-40
-
-
Hayot, C.1
-
36
-
-
0037082333
-
Capillary plexus development in the day five to day six chick chorioallantoic membrane is inhibited by cytochalasin D and suramin
-
Melkonian, G. et al. Capillary plexus development in the day five to day six chick chorioallantoic membrane is inhibited by cytochalasin D and suramin. J. Exp. Zool. 292, 241-254 (2002).
-
(2002)
J. Exp. Zool
, vol.292
, pp. 241-254
-
-
Melkonian, G.1
-
37
-
-
35948954029
-
High tumoral levels of Kiss1 and G-protein-coupled receptor 54 expression are correlated with poor prognosis of estrogen receptor-positive breast tumors
-
Marot, D. et al. High tumoral levels of Kiss1 and G-protein-coupled receptor 54 expression are correlated with poor prognosis of estrogen receptor-positive breast tumors. Endocr. Relat. Cancer 14, 691-702 (2007).
-
(2007)
Endocr. Relat. Cancer
, vol.14
, pp. 691-702
-
-
Marot, D.1
-
38
-
-
34147181120
-
Mutant transcription factors and tyrosine kinases as therapeutic targets for leukemias: From acute promyelocytic leukemia to chronic myeloid leukemia and beyond
-
Hu, J., Zhou, G.B., Wang, Z.Y., Chen, S.J. & Chen, Z. Mutant transcription factors and tyrosine kinases as therapeutic targets for leukemias: from acute promyelocytic leukemia to chronic myeloid leukemia and beyond. Adv. Cancer Res. 98, 191-220 (2007).
-
(2007)
Adv. Cancer Res
, vol.98
, pp. 191-220
-
-
Hu, J.1
Zhou, G.B.2
Wang, Z.Y.3
Chen, S.J.4
Chen, Z.5
-
39
-
-
0037224547
-
The phosphoinositide 3-kinase/AKT1 pathway involvement in drug and all-trans-retinoic acid resistance of leukemia cells
-
Neri, L.M. et al. The phosphoinositide 3-kinase/AKT1 pathway involvement in drug and all-trans-retinoic acid resistance of leukemia cells. Mol. Cancer Res. 1, 234-246 (2003).
-
(2003)
Mol. Cancer Res
, vol.1
, pp. 234-246
-
-
Neri, L.M.1
-
40
-
-
13944284494
-
Oncogenic mutations of PIK3CA in human cancers
-
Samuels, Y. & Velculescu, V.E. Oncogenic mutations of PIK3CA in human cancers. Cell Cycle 3, 1221-1224 (2004).
-
(2004)
Cell Cycle
, vol.3
, pp. 1221-1224
-
-
Samuels, Y.1
Velculescu, V.E.2
-
41
-
-
0026316082
-
All-trans retinoic acid modulates the retinoic acid receptor-alpha in promyelocytic cells
-
Chomienne, C. et al. All-trans retinoic acid modulates the retinoic acid receptor-alpha in promyelocytic cells. J. Clin. Invest. 88, 2150-2154 (1991).
-
(1991)
J. Clin. Invest
, vol.88
, pp. 2150-2154
-
-
Chomienne, C.1
-
42
-
-
0026735778
-
Mechanisms of multidrug resistance in cancer treatment
-
Harris, A.L. & Hochhauser, D. Mechanisms of multidrug resistance in cancer treatment. Acta Oncol. 31, 205-213 (1992).
-
(1992)
Acta Oncol
, vol.31
, pp. 205-213
-
-
Harris, A.L.1
Hochhauser, D.2
-
43
-
-
0027053839
-
Etoposide pharmacology
-
Hande, K.R. Etoposide pharmacology. Semin. Oncol. 19, 3-9 (1992).
-
(1992)
Semin. Oncol
, vol.19
, pp. 3-9
-
-
Hande, K.R.1
-
44
-
-
23644450562
-
Combined effects of GSTP1 and MRP1 in melanoma drug resistance
-
Depeille, P., Cuq, P., Passagne, I., Evrard, A. & Vian, L. Combined effects of GSTP1 and MRP1 in melanoma drug resistance. Br. J. Cancer 93, 216-223 (2005).
-
(2005)
Br. J. Cancer
, vol.93
, pp. 216-223
-
-
Depeille, P.1
Cuq, P.2
Passagne, I.3
Evrard, A.4
Vian, L.5
-
45
-
-
33845906363
-
The effect of low pH on breast cancer resistance protein (ABCG2)-mediated transport of methotrexate, 7-hydroxymethotrexate, methotrexate diglutamate, folic acid, mitoxantrone, topotecan, and resveratrol in in vitro drug transport models
-
Breedveld, P. et al. The effect of low pH on breast cancer resistance protein (ABCG2)-mediated transport of methotrexate, 7-hydroxymethotrexate, methotrexate diglutamate, folic acid, mitoxantrone, topotecan, and resveratrol in in vitro drug transport models. Mol. Pharmacol. 71, 240-249 (2007).
-
(2007)
Mol. Pharmacol
, vol.71
, pp. 240-249
-
-
Breedveld, P.1
-
46
-
-
0029098798
-
An etoposide-resistant lung cancer subline overexpresses the multidrug resistance-associated protein
-
Doyle, L.A. et al. An etoposide-resistant lung cancer subline overexpresses the multidrug resistance-associated protein. Br. J. Cancer 72, 535-542 (1995).
-
(1995)
Br. J. Cancer
, vol.72
, pp. 535-542
-
-
Doyle, L.A.1
-
47
-
-
0033028596
-
Systematic determination of genetic network architecture
-
Tavazoie, S., Hughes, J.D., Campbell, M.J., Cho, R.J. & Church, G.M. Systematic determination of genetic network architecture. Nat. Genet. 22, 281-285 (1999).
-
(1999)
Nat. Genet
, vol.22
, pp. 281-285
-
-
Tavazoie, S.1
Hughes, J.D.2
Campbell, M.J.3
Cho, R.J.4
Church, G.M.5
-
48
-
-
30844461216
-
Finding biological process modifications in cancer tissues by mining gene expression correlations
-
Gamberoni, G., Storari, S. & Volinia, S. Finding biological process modifications in cancer tissues by mining gene expression correlations. BMC Bioinformatics 7, 6 (2006).
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 6
-
-
Gamberoni, G.1
Storari, S.2
Volinia, S.3
|