Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data

Nucleic Acids Research

Volumn 38, Issue 11, 2010, Pages

  Essaghir, Ahmed ^a   Toffalini, Federica ^a   Knoops, Laurent ^a,b   Kallin, Anders ^a   van Helden, Jacques ^c   Demoulin, Jean Baptiste ^a  

^a DE DUVE INSTITUTE   (Belgium)

^b CLINIQUES UNIVERSITAIRES SAINT LUC   (Belgium)

^c UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIN; BASIC FIBROBLAST GROWTH FACTOR; EARLY GROWTH RESPONSE FACTOR 1; HYPOXIA INDUCIBLE FACTOR 1; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; MICROPHTHALMIA ASSOCIATED TRANSCRIPTION FACTOR; MYC PROTEIN; PLATELET DERIVED GROWTH FACTOR BB; PROTEIN KINASE B; PROTEIN P53; SMAD PROTEIN; STAT PROTEIN; STAT1 PROTEIN; STAT3 PROTEIN; STEROL REGULATORY ELEMENT BINDING PROTEIN; STRESS ACTIVATED PROTEIN KINASE; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR AP 1; TRANSCRIPTION FACTOR E2F; TRANSCRIPTION FACTOR FKHRL1; TRANSCRIPTION FACTOR JUN; TRANSCRIPTION FACTOR SOX10; TRANSCRIPTION FACTOR SP1; UNCLASSIFIED DRUG;

ACCURACY; ARTICLE; CELL STIMULATION; COMPUTER MODEL; COMPUTER PROGRAM; CONTROLLED STUDY; DATA MINING; FIBROBLAST; GENE EXPRESSION PROFILING; GENE TARGETING; GENETIC ANALYSIS; GENETIC REGULATION; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; PREDICTION; PRIORITY JOURNAL; PROMOTER REGION; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION;

CATALOGS AS TOPIC; CELL LINE, TUMOR; CELLS, CULTURED; DATA INTERPRETATION, STATISTICAL; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLATELET-DERIVED GROWTH FACTOR; REPRODUCIBILITY OF RESULTS; SOFTWARE; STAT TRANSCRIPTION FACTORS; TRANSCRIPTION FACTORS; USER-COMPUTER INTERFACE;

EID: 77954364953     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq149     Document Type: Article

References (58)

1. Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gillette, M.A., Paulovich, A., Pomeroy, S.L., Golub, T.R., Lander, E.S. et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA, 102, 15545-15550.
2. Defrance, M. and Touzet, H. (2006) Predicting transcription factor binding sites using local over-representation and comparative genomics. BMC Bioinformatics, 7, 396.
3. Hestand, M.S., van Galen, M., Villerius, M.P., van Ommen, G.J., den Dunnen, J.T. and 't Hoen, P.A. (2008) CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes. BMC Bioinformatics, 9, 384.
4. Liu, C.C., Lin, C.C., Chen, W.S.E., Chen, H.Y., Chang, P.C., Chen, J.J.W. and Yang, P.C. (2006) CRSD: a comprehensive web server for composite regulatory signature discovery. Nucleic Acids Res., 34, W571-W577.
5. Ho Sui, S.J., Mortimer, J.R., Arenillas, D.J., Brumm, J., Walsh, C.J., Kennedy, B.P. and Wasserman, W.W. (2005) oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes. Nucleic Acids Res., 33, 3154-3164.
6. Sand, O., Turatsinze, J.V. and van Helden, J. (2008) Modern Genome Annotation: the BioSapiens Network. Springer, Vienna, Austria.
7. Veerla, S. and Höglund, M. (2006) Analysis of promoter regions of co-expressed genes identified by microarray analysis. BMC Bioinformatics, 7.
8. Werner, T. (2008) Bioinformatics applications for pathway analysis of microarray data. Curr. Opin. Biotechnol., 19, 50-54.
9. Elemento, O., Slonim, N. and Tavazoie, S. (2007) A universal framework for regulatory element discovery across all genomes and data types. Mol. Cell, 28, 337-350.
10. Sinha, S., Adler, A.S., Field, Y., Chang, H.Y. and Segal, E. (2008) Systematic functional characterization of cis-regulatory motifs in human core promoters. Genome Res., 18, 477-488.
11. Linhart, C., Halperin, Y. and Shamir, R. (2008) Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets. Genome Res., 18, 1180-1189.
12. The FANTOM Consortium and Riken Omics Science Center. (2009) The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat. Genet., 41, 553-562.
13. Demoulin, J.B., Ericsson, J., Kallin, A., Rorsman, C., Rönnstrand, L. and Heldin, C.H. (2004) Platelet-derived growth factor stimulates membrane lipid synthesis through activation of phosphatidylinositol 3-kinase and sterol regulatory element-binding proteins. J. Biol. Chem., 279, 35392-35402.
14. Kallin, A., Johannessen, L.E., Cani, P.D., Marbehant, C.Y., Essaghir, A., Foufelle, F., Ferré, P., Heldin, C.H., Delzenne, N.M. and Demoulin, J.B. (2007) SREBP-1 regulates the expression of heme oxygenase 1 and the phosphatidylinositol-3 kinase regulatory subunit p55 gamma. J. Lipid Res., 48, 1628-1636.
15. Knoops, L., Haas, R., de Kemp, S., Majoor, D., Broeks, A., Eldering, E., de Boer, J.P., Verheij, M., van Ostrom, C., de Vries, A. et al. (2007) In vivo p53 response and immune reaction underlie highly effective low-dose radiotherapy in follicular lymphoma. Blood, 110, 1116-1122.
16. Grazul-Bilska, A.T., Johnson, M.L., Bilski, J.J., Redmer, D.A., Reynolds, L.P., Abdullah, A. and Abdullah, K.M. (2003) Wound healing: the role of growth factors. Drugs Today (Barc), 39, 787-800.
17. Demoulin, J.B., Enarsson, M., Larsson, J., Essaghir, A., Heldin, C.H. and Forsberg-Nilsson, K. (2006) The gene expression profile of PDGF-treated neural stem cells corresponds to partially differentiated neurons and glia. Growth Factors, 24, 184-196.
18. Fambrough, D., McClure, K., Kazlauskas, A. and Lander, E.S. (1999) Diverse signaling pathways activated by growth factor receptors induce broadly overlapping, rather than independent, sets of genes. Cell, 97, 727-741.
19. Zhao, F., Xuan, Z., Liu, L. and Zhang, M.Q. (2007) TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. Nucleic Acids Res., 35, 137-140.
20. Kel', A.E., Kolchanov, N.A., Kel', O.V., Romashchenko, A.G., Anan'ko, E.A., Ignat'eva, E.V., Merkulova, T.I., Podkolodnaia, O.A., Stepanenko, I.L., Kochetov, A.V. et al. (1997) TRRD: a database of transcription regulatory regions in eukaryotic genes. Mol. Biol. (Mosk), 31, 626-636.
21. Portales-Casamar, E., Kirov, S., Lim, J., Lithwick, S., Swanson, M.I., Ticoll, A., Snoddy, J. and Wasserman, W.W. (2007) PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation. Genome Biol., 8, R207.
22. Storey, J.D. and Tibshirani, R. (2003) Statistical significance for genomewide studies. Proc. Natl Acad. Sci. USA, 100, 9440-9445.
23. Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Stat. Soc., 57, 289-300.
24. Shankavaram, U.T., Reinhold, W.C., Nishizuka, S., Major, S., Morita, D., Chary, K.K., Reimers, M.A., Scherf, U., Kahn, A., Dolginow, D. et al. (2007) Transcript and protein expression profiles of the NCI-60 cancer cell panel: an integromic microarray study. Mol. Cancer Ther., 6, 820-832.
25. Essaghir, A., Dif, N., Marbehant, C.Y., Coffer, P.J. and Demoulin, J.B. (2009) The transcription of FOXO genes is stimulated by FOXO3 and repressed by growth factors. J. Biol. Chem., 284, 10334-10342.
26. Leja, J., Essaghir, A., Essand, M., Wester, K., Oberg, K., Totterman, T.H., Lloyd, R., Vasmatzis, G., Demoulin, J.B. and Giandomenico, V. (2009) Novel markers for enterochromaffin cells and gastrointestinal neuroendocrine carcinomas. Mod. Pathol., 22, 261-272.
27. Saeed, A.I., Sharov, V., White, J., Li, J., Liang, W., Bhagabati, N., Braisted, J., Klapa, M., Currier, T., Thiagarajan, M. et al. (2003) TM4: a free, open-source system for microarray data management and analysis. Biotechniques, 34, 374-378.
28. Cools, J., Quentmeier, H., Huntly, B.J., Marynen, P., Griffin, J.D., Drexler, H.G. and Gilliland, D.G. (2004) The EOL-1 cell line as an in vitro model for the study of FIP1L1-PDGFRA-positive chronic eosinophilic leukemia. Blood, 103, 2802-2805.
29. Chiara, F., Bishayee, S., Heldin, C.H. and Demoulin, J.B. (2004) Autoinhibition of the platelet-derived growth factor beta-receptor tyrosine kinase by its C-terminal tail. J. Biol. Chem., 279, 19732-19738.
30. Demoulin, J.B., Seo, J.K., Ekman, S., Grapengiesser, E., Hellman, U., Rönnstrand, L. and Heldin, C.H. (2003) Ligand-induced recruitment of Na+/H+-exchanger regulatory factor to the PDGF (platelet-derived growth factor) receptor regulates actin cytoskeleton reorganization by PDGF. Biochem. J., 376(Pt 2), 505-510.
31. Toffalini, F., Kallin, A., Vandenberghe, P., Pierre, P., Michaux, L., Cools, J. and Demoulin, J.B. (2009) The fusion proteins TEL-PDGFRbeta and FIP1L1-PDGFRalpha escape ubiquitination and degradation. Haematologica, 94, 1085-1093.
32. Terragni, J., Graham, J.R., Adams, K.W., Schaffer, M.E., Tullai, J.W. and Cooper, G.M. (2008) Phosphatidylinositol 3-kinase signaling in proliferating cells maintains an anti-apoptotic transcriptional program mediated by inhibition of FOXO and non-canonical activation of NF-ΚB transcription factors. BMC Cell Biol., 9, 6.
33. Delpuech, O., Griffiths, B., East, P., Essafi, A., Lam, E.W.F., Burgering, B., Downward, J. and Schulze, A. (2007) Induction of Mxi1-SR by FOXO3a contributes to repression of Myc-dependent gene expression. Mol. Cell. Biol., 27, 4917-4930.
34. Coller, H.A., Grandori, C., Tamayo, P., Colbert, T., Lander, E.S., Eisenman, R.N. and Golub, T.R. (2000) Expression analysis with oligonucleotide microarrays reveals that MYC regulates genes involved in growth, cell cycle, signaling, and adhesion. Proc. Natl Acad. Sci. USA, 97, 3260-3265.
35. Der, S.D., Zhou, A., Williams, B.R.G. and Silverman, R.H. (2001) Identification of genes differentially regulated by interferon, or using oligonucleotide arrays. Proc. Natl Acad. Sci. USA, 95, 15623-15628.
36. Kannan, K., Amariglio, N., Rechavi, G., Jakob-Hirsch, J., Kela, I., Kaminski, N., Getz, G., Domany, E. and Givol, D. (2001) DNA microarrays identification of primary and secondary target genes regulated by p53. Oncogene, 20, 2225-2234.
37. Ma, D., Nutt, C.L., Shanehsaz, P., Peng, X., Louis, D.N. and Kaetzel, D.M. (2005) Autocrine PDGFa dependent gene expression in glioblastoma is mediated largely by activation of SREBP and is associated with altered genotype and patient survival in human brain tumors. Cancer Res., 65, 5523-5534.
38. Theilgaard-Monch, K., Knudsen, S., Follin, P. and Borregaard, N. (2004) The Transcriptional activation program of human neutrophils in skin lesions supports their important role in wound healing. J. Immunol., 172, 7684-7693.
39. Basso, K., Klein, U., Niu, H., Stolovitzky, G.A., Tu, Y., Califano, A., Cattoretti, G. and Dalla-Favera, R. (2004) Tracking CD40 signaling during germinal center development. Blood, 104, 4088-4096.
40. Peng, T., Golub, T.R. and Sabatini, D.M. (2002) The Immunosuppressant Rapamycin Mimics a starvation-like signal distinct from amino acid and glucose deprivation. Mol. Cell. Biol., 22, 5575-5584.
41. Doghman, M., Karpova, T., Rodrigues, G.A., Arhatte, M., De Moura, J., Cavalli, L.R., Virolle, V., Barbry, P., Zambetti, G.P., Figueiredo, B.C. et al. (2007) Increased steroidogenic factor-1 dosage triggers adrenocortical cell proliferation and cancer. Mol. Endocrinol., 21, 2968-2987.
42. Fu, M., Zhu, X., Zhang, J., Liang, J., Lin, Y., Zhao, L., Ehrengruber, M.U. and Chen, Y.E. (2003) Egr-1 target genes in human endothelial cells identified by microarray analysis. Gene, 315, 33-41.
43. Pohlers, D., Beyer, A., Koczan, D., Wilhelm, T., Thiesen, H.J. and Kinne, R.W. (2007) Constitutive upregulation of the transforming growth factor-beta pathway in rheumatoid arthritis synovial fibroblasts. Arthritis Res. Ther., 9, R59.
44. van de Sluis, B., Muller, P., Duran, K., Chen, A., Groot, A.J., Klomp, L.W., Liu, P.P. and Wijmenga, C. (2007) Increased activity of hypoxia-inducible factor 1 is associated with early embryonic lethality in Commd1 null mice. Mol. Cell. Biol., 27, 4142-4156.
45. Tatsukawa, H., Fukaya, Y., Frampton, G., Martinez-Fuentes, A., Suzuki, K., Kuo, T.F., Nagatsuma, K., Shimokado, K., Okuno, M., Wu, J. et al. (2009) Role of transglutaminase 2 in liver injury via cross-linking and silencing of transcription factor Sp1. Gastroenterology, 136, 1783-1795.
46. Vernell, R., Helin, K. and Müller, H. (2003) Identification of target genes of the p16INK4A-pRB-E2F pathway. J. Biol. Chem., 278, 46124-46137.
47. Zhang, J.Y., Adams, A.E., Ridky, T.W., Tao, S. and Khavari, P.A. (2007) Tumor necrosis factor receptor 1/c-Jun-NH2-kinase signaling promotes human neoplasia. Cancer Res., 67, 3827-3834.
48. Wingender, E. (2008) The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Brief Bioinform., 9, 326-332.
49. Sandelin, A., Alkema, W., Engström, P., Wasserman, W.W. and Lenhard, B. (2004) JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res, 32, D91-D94.
50. Karin, M. (1995) The regulation of AP-1 activity by mitogen-activated protein kinases. J. Biol. Chem., 270, 16483-16486.
51. Molina, D.M., Grewal, S. and Bardwell, L. (2005) Characterization of an ERK-binding domain in microphthalmia-associated transcription factor and differential inhibition of ERK2-mediated substrate phosphorylation. J. Biol. Chem., 280, 42051-42060.
52. Pan, J., Quintàs-Cardama, A., Manshouri, T., Giles, F.J., Lamb, P., Tefferi, A., Cortes, J., Kantarjian, H. and Verstovsek, S. (2007) The novel tyrosine kinase inhibitor EXEL-0862 induces apoptosis in human FIP1L1-PDGFR-alpha-expressing cells through caspase-3-mediated cleavage of Mcl-1. Leukemia, 21, 1395-1404.
53. Seifert, M., Scherf, M., Epple, A. and Werner, T. (2005) Multievidence microarray mining. Trends Genet., 21, 553-558.
54. Bowman, T., Broome, M.A., Sinibaldi, D., Wharton, W., Pledger, W.J., Sedivy, J.M., Irby, R., Yeatman, T., Courtneidge, S.A. and Jove, R. (2001) Stat3-mediated Myc expression is required for Src transformation and PDGF-induced mitogenesis. Proc. Natl Acad. Sci. USA, 98, 7319-7324.
55. Quesnelle, K.M., Boehm, A.L. and Grandis, J.R. (2007) STAT-mediated EGFR signaling in cancer. J. Cell. Biochem., 102, 311-319.
56. Himpe, E. and Kooijman, R. (2009) Insulin-like growth factor-i receptor signal transduction and the janus kinase/signal transducer and activator of transcription (JAK-STAT) pathway. Biofactors, 35, 76-81.
57. Yang, X., Qiao, D., Meyer, K. and Friedl, A. (2009) Signal transducers and activators of transcription mediate fibroblast growth factor-induced vascular endothelial morphogenesis. Cancer Res., 69, 1668-1677.
58. Montgomery, S.B., Griffith, O.L., Sleumer, M.C., Bergman, C.M., Bilenky, M., Pleasance, E.D., Prychyna, Y., Zhang, X. and Jones, S.J. (2006) ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. Bioinformatics, 22, 637-640.