TcoF-DB: Dragon database for human transcription co-factors and transcription factor interacting proteins

Nucleic Acids Research

Volumn 39, Issue SUPPL. 1, 2011, Pages

  Schaefer, Ulf ^a   Schmeier, Sebastian ^a   Bajic, Vladimir B ^a  

^a KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Saudi Arabia)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION CO FACTOR; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ARTICLE; CELL NUCLEUS; COMPUTER INTERFACE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; TCOF DB; TRANSCRIPTION REGULATION; WEB BROWSER;

EUKARYOTA;

EID: 78651294477     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq945     Document Type: Article

References (45)

1. Ravasi, T., Suzuki, H., Cannistraci, C.V., Katayama, S., Bajic, V.B., Tan, K., Akalin, A., Schmeier, S., Kanamori-Katayama, M., Bertin, N. et al. (2010) An atlas of combinatorial transcriptional regulation in mouse and man. Cell, 140, 744-752.
2. Lemon, B. and Tjian, R. (2000) Orchestrated response: A symphony of transcription factors for gene control. Genes Dev., 14, 2551-2569.
3. Lee, T.I. and Young, R.A. (2000) Transcription of eukaryotic protein-coding genes. Annu. Rev. Genet., 34, 77-137.
4. Nikolov, D.B. and Burley, S.K. (1997) RNA polymerase II transcription initiation: A structural view. Proc. Natl Acad. Sci. USA, 94, 15-22.
5. Mitchell, P.J. and Tjian, R. (1989) Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins. Science, 245, 371-378.
6. Gamble, M. (2002) A coactivator code for transcription. Trends Biochem. Sci., 27, 165-167.
7. Roeder, R.G. (1998) Role of general and gene-specific cofactors in the regulation of eukaryotic transcription. Cold Spring Harb. Symp. Quant. Biol., 63, 201-218.
8. Latchman, D.S. (1997) Transcription factors: An overview. Int. J. Biochem. Cell Biol., 29, 1305-1312.
9. Gill, G. (2001) Regulation of the initiation of eukaryotic transcription. Essays Biochem., 37, 33-43.
10. Xu, L., Glass, C. and Rosenfeld, M. (1999) Coactivator and corepressor complexes in nuclear receptor function. Curr. Opin. Genet. Dev., 9, 140-147.
11. Thomas, M.C. and Chiang, C. The general transcription machinery and general cofactors. Crit. Rev. Biochem. Mol. Biol., 41, 105-178.
12. Martinez, E. (2002) Multi-protein complexes in eukaryotic gene transcription. Plant Mol. Biol., 50, 925-947.
13. Vaquerizas, J.M., Kummerfeld, S.K., Teichmann, S.A. and Luscombe, N.M. (2009) A census of human transcription factors: Function, expression and evolution. Nat. Rev. Genet., 10, 252-263.
14. Engelkamp, D. and van Heyningen, V. (1996) Transcription factors in disease. Curr. Opin. Genet. Dev., 6, 334-342.
15. Mauro, C., Zazzeroni, F., Papa, S., Bubici, C. and Franzoso, G. (2009) The NF-kappaB transcription factor pathway as a therapeutic target in cancer: Methods for detection of NF-kappaB activity. Methods Mol. Biol., 512, 169-207.
16. Morgan, R., Plowright, L., Harrington, K.J., Michael, A. and Pandha, H.S. (2010) Targeting HOX and PBX transcription factors in ovarian cancer. BMC Cancer, 10, 89.
17. Wang, C., Chen, J.J. and Yang, P. (2006) Multifunctional transcription factor YY1: A therapeutic target in human cancer? Expert Opin. Ther. Targets, 10, 253-266.
18. Lu, H. and Huan, C. (2007) Transcription factor NFAT, its role in cancer development, and as a potential target for chemoprevention. Curr. Cancer Drug Targets, 7, 343-353.
19. Kothandaraman, N., Bajic, V.B., Brendan, P.N., Huak, C.Y., Keow, P.B., Razvi, K., Salto-Tellez, M. and Choolani, M. (2010) E2F5 status significantly improves malignancy diagnosis of epithelial ovarian cancer. BMC Cancer, 10, 64.
20. Cuadrado, A., Moreno-Murciano, P. and Pedraza-Chaverri, J. (2009) The transcription factor Nrf2 as a new therapeutic target in Parkinson's disease. Expert Opin. Ther. Targets, 13, 319-329.
21. Qian, L., Mohapatra, B., Akasaka, T., Liu, J., Ocorr, K., Towbin, J.A. and Bodmer, R. (2008) Transcription factor neuromancer/TBX20 is required for cardiac function in Drosophila with implications for human heart disease. Proc. Natl Acad. Sci. USA, 105, 19833-19838.
22. Desplats, P.A., Lambert, J.R. and Thomas, E.A. (2008) Functional roles for the striatal-enriched transcription factor, Bcl11b, in the control of striatal gene expression and transcriptional dysregulation in Huntington's disease. Neurobiol. Dis., 31, 298-308.
23. Citron, B.A., Dennis, J.S., Zeitlin, R.S. and Echeverria, V. (2008) Transcription factor Sp1 dysregulation in Alzheimer's disease. J. Neurosci. Res., 86, 2499-24504.
24. Xia, K., Fu, Z., Hou, L. and Han, J.J. (2008) Impacts of protein-protein interaction domains on organism and network complexity. Genome Res., 18, 1500-1508.
25. Giangrande, P.H., Kimbrel, E.A., Edwards, D.P. and McDonnell, D.P. (2000) The opposing transcriptional activities of the two isoforms of the human progesterone receptor are due to differential cofactor binding. Mol. Cell. Biol., 20, 3102-3115.
26. The UniProt Consortium (2010) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res., 38, D142-D148.
27. Keshava Prasad, T.S., Goel, R., Kandasamy, K., Keerthikumar, S., Kumar, S., Mathivanan, S., Telikicherla, D., Raju, R., Shafreen, B., Venugopal, A. et al. (2009) Human protein reference database- 2009 update. Nucleic Acids Res., 37, D767-D772.
28. Pontén, F., Jirström, K. and Uhlen, M. (2008) The human protein atlas-a tool for pathology. J. Pathol., 216, 387-393.
29. Kandasamy, K., Keerthikumar, S., Goel, R., Mathivanan, S., Patankar, N., Shafreen, B., Renuse, S., Pawar, H., Ramachandra, Y.L., Acharya, P.K. et al. (2009) Human Proteinpedia: A unified discovery resource for proteomics research. Nucleic Acids Res., 37, D773-D781.
30. Breitkreutz, B., Stark, C., Reguly, T., Boucher, L., Breitkreutz, A., Livstone, M., Oughtred, R., Lackner, D.H., Bähler, J., Wood, V. et al. (2008) The BioGRID interaction database: 2008 update. Nucleic Acids Res., 36, D637-D640.
31. Aranda, B., Achuthan, P., Alam-Faruque, Y., Armean, I., Bridge, A., Derow, C., Feuermann, M., Ghanbarian, A.T., Kerrien, S., Khadake, J. et al. (2010) The IntAct molecular interaction database in 2010. Nucleic Acids Res., 38, D525-D531.
32. Pagel, P., Kovac, S., Oesterheld, M., Brauner, B., Dunger- Kaltenbach, I., Frishman, G., Montrone, C., Mark, P., Stümpflen, V., Mewes, H. et al. (2005) The MIPS mammalian protein-protein interaction database. Bioinformatics, 21, 832-834.
33. Han, K., Park, B., Kim, H., Hong, J. and Park, J. (2004) HPID: The human protein interaction database. Bioinformatics, 20, 2466-2470.
34. Matys, V., Kel-Margoulis, O.V., Fricke, E., Liebich, I., Land, S., Barre-Dirrie, A., Reuter, I., Chekmenev, D., Krull, M., Hornischer, K. et al. (2006) TRANSFAC and its module TRANSCompel: Transcriptional gene regulation in eukaryotes. Nucleic Acids Res., 34, D108-D110.
35. Wilson, D., Charoensawan, V., Kummerfeld, S.K. and Teichmann, S.A. (2008) DBD-taxonomically broad transcription factor predictions: New content and functionality. Nucleic Acids Res., 36, D88-D92.
36. Kanamori, M., Konno, H., Osato, N., Kawai, J., Hayashizaki, Y. and Suzuki, H. (2004) A genome-wide and nonredundant mouse transcription factor database. Biochem. Biophys. Res. Commun., 322, 787-793.
37. Fulton, D.L., Sundararajan, S., Badis, G., Hughes, T.R., Wasserman, W.W., Roach, J.C. and Sladek, R. (2009) TFCat: The curated catalog of mouse and human transcription factors. Genome Biol., 10, R29.
38. Sayers, E.W., Barrett, T., Benson, D.A., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., DiCuccio, M., Edgar, R., Federhen, S. et al. (2009) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 37, D5-D15.
39. Ceol, A., Chatr Aryamontri, A., Licata, L., Peluso, D., Briganti, L., Perfetto, L., Castagnoli, L. and Cesareni, G. (2010) MINT, the molecular interaction database: 2009 update. Nucleic Acids Res., 38, D532-D539.
40. Matthews, L., Gopinath, G., Gillespie, M., Caudy, M., Croft, D., de Bono, B., Garapati, P., Hemish, J., Hermjakob, H., Jassal, B. et al. (2009) Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res., 37, D619-D622.
41. Orchard, S. and Kerrien, S. (2010) Molecular interactions and data standardisation. Methods Mol. Biol., 604, 309-318.
42. The Gene Ontology Consortium (2010) The Gene Ontology in 2010: Extensions and refinements. Nucleic Acids Res., 38, D331-D335.
43. Carbon, S., Ireland, A., Mungall, C.J., Shu, S., Marshall, B. and Lewis, S. (2009) AmiGO: Online access to ontology and annotation data. Bioinformatics, 25, 288-289.
44. Mathivanan, S., Periaswamy, B., Gandhi, T.K., Kandasamy, K., Suresh, S., Mohmood, R., Ramachandra, Y.L. and Pandey, A. (2006) An evaluation of human protein-protein interaction data in the public domain. BMC Bioinformatics, 7(Suppl 5), S19.
45. Babu, M.M., Luscombe, N.M., Aravind, L., Gerstein, M. and Teichmann, S.A. (2004) Structure and evolution of transcriptional regulatory networks. Curr. Opin. Struct. Biol., 14, 283-291.