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TFCat: the curated catalog of mouse and human transcription factors

Fulton, Debra L, Sundararajan, Saravanan, Badis, Gwenael, Hughes, Timothy R, Wasserman, Wyeth W, Roach, Jared C, Sladek, Rob·2009·Genome Biology
DOI 10.1186/gb-2009-10-3-r29PMC PMC2691000
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Abstract

Unravelling regulatory programs governed by transcription factors (TFs) is fundamental to understanding biological systems. TFCat is a catalog of mouse and human TFs based on a reliable core collection of annotations obtained by expert review of the scientific literature. The collection, including proven and homology-based candidate TFs, is annotated within a function-based taxonomy and DNA-binding proteins are organized within a classification system. All data and user-feedback mechanisms are available at the TFCat portal http://www.tfcat.ca.

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Research works printed but not linked: 61

  1. Garvie CW, Wolberger C: Recognition of specific DNA sequences. Mol Cell. 2001, 8: 937-946. 10.1016/S1097-2765(01)00392-6. · DOI · Paper page
  2. Halford SE, Marko JF: How do site-specific DNA-binding proteins find their targets?. Nucleic Acids Res. 2004, 32: 3040-3052. 10.1093/nar/gkh624. · DOI · Paper page
  3. Rescan PY: Regulation and functions of myogenic regulatory factors in lower vertebrates. Comp Biochem Physiol B Biochem Mol Biol. 2001, 130: 1-12. 10.1016/S1096-4959(01)00412-2. · DOI
  4. Latchman DS: Eukaryotic Transcription Factors. 2004, London, San Diego, CA: Elsevier Academic Press
  5. Locker J: Transcription Factors. 2001, Oxford, San Diego, CA: Bios, Academic Press
  6. Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA: Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol. 2004, 14: 283-291. 10.1016/j.sbi.2004.05.004. · DOI
  7. Gray PA, Fu H, Luo P, Zhao Q, Yu J, Ferrari A, Tenzen T, Yuk DI, Tsung EF, Cai Z, Alberta JA, Cheng LP, Liu Y, Stenman JM, Valerius MT, Billings N, Kim HA, Greenberg ME, McMahon AP, Rowitch DH, Stiles CD, Ma Q: Mouse brain organization revealed through direct genome-scale TF expression analysis. Science. 2004, 306: 2255-2257. 10.1126/science.1104935. · DOI · Paper page
  8. Huntley S, Baggott DM, Hamilton AT, Tran-Gyamfi M, Yang S, Kim J, Gordon L, Branscomb E, Stubbs L: A comprehensive catalog of human KRAB-associated zinc finger genes: insights into the evolutionary history of a large family of transcriptional repressors. Genome Res. 2006, 16: 669-677. 10.1101/gr.4842106. · DOI · Paper page
  9. Messina DN, Glasscock J, Gish W, Lovett M: An ORFeome-based analysis of human transcription factor genes and the construction of a microarray to interrogate their expression. Genome Res. 2004, 14: 2041-2047. 10.1101/gr.2584104. · DOI
  10. Bateman A, Birney E, Durbin R, Eddy SR, Finn RD, Sonnhammer EL: Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucleic Acids Res. 1999, 27: 260-262. 10.1093/nar/27.1.260. · DOI · Paper page
  11. Gough J: The SUPERFAMILY database in structural genomics. Acta Crystallogr D Biol Crystallogr. 2002, 58: 1897-1900. 10.1107/S0907444902015160. · DOI
  12. Adryan B, Teichmann SA: FlyTF: a systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster. Bioinformatics. 2006, 22: 1532-1533. 10.1093/bioinformatics/btl143. · DOI
  13. Xi H, Shulha HP, Lin JM, Vales TR, Fu Y, Bodine DM, McKay RD, Chenoweth JG, Tesar PJ, Furey TS, Ren B, Weng Z, Crawford GE: Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet. 2007, 3: e136-10.1371/journal.pgen.0030136. · DOI
  14. Luscombe NM, Austin SE, Berman HM, Thornton JM: An overview of the structures of protein-DNA complexes. Genome Biol. 2000, 1: REVIEWS001-10.1186/gb-2000-1-1-reviews001. · DOI
  15. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Geer LY, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Ostell J, Miller V, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2007, 35: D5-12. 10.1093/nar/gkl1031. · DOI · Paper page
  16. Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE: The mouse genome database (MGD): new features facilitating a model system. Nucleic Acids Res. 2007, 35: D630-637. 10.1093/nar/gkl940. · DOI
  17. Coulier F, Popovici C, Villet R, Birnbaum D: MetaHox gene clusters. J Exp Zool. 2000, 288: 345-351. 10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y. · DOI
  18. Marchler-Bauer A, Anderson JB, Derbyshire MK, DeWeese-Scott C, Gonzales NR, Gwadz M, Hao L, He S, Hurwitz DI, Jackson JD, Ke Z, Krylov D, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Thanki N, Yamashita RA, Yin JJ, Zhang D, Bryant SH: CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res. 2007, 35: D237-240. 10.1093/nar/gkl951. · DOI · Paper page
  19. Murzin AG, Brenner SE, Hubbard T, Chothia C: SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol. 1995, 247: 536-540.
  20. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM: CATH-a hierarchic classification of protein domain structures. Structure. 1997, 5: 1093-1108. 10.1016/S0969-2126(97)00260-8. · DOI · Paper page
  21. Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M: The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977, 112: 535-542. 10.1016/S0022-2836(77)80200-3. · DOI
  22. Laity JH, Lee BM, Wright PE: Zinc finger proteins: new insights into structural and functional diversity. Curr Opin Struct Biol. 2001, 11: 39-46. 10.1016/S0959-440X(00)00167-6. · DOI · Paper page
  23. Nagadoi A, Nakazawa K, Uda H, Okuno K, Maekawa T, Ishii S, Nishimura Y: Solution structure of the transactivation domain of ATF-2 comprising a zinc finger-like subdomain and a flexible subdomain. J Mol Biol. 1999, 287: 593-607. 10.1006/jmbi.1999.2620. · DOI
  24. Stefancsik R, Sarkar S: Relationship between the DNA binding domains of SMAD and NFI/CTF transcription factors defines a new superfamily of genes. DNA Sequence. 2003, 14: 233-239. · DOI
  25. Rekdal C, Sjottem E, Johansen T: The nuclear factor SPBP contains different functional domains and stimulates the activity of various transcriptional activators. J Biol Chem. 2000, 275: 40288-40300. 10.1074/jbc.M006978200. · DOI
  26. Horn G, Hofweber R, Kremer W, Kalbitzer HR: Structure and function of bacterial cold shock proteins. Cell Mol Life Sci. 2007, 64: 1457-1470. 10.1007/s00018-007-6388-4. · DOI · Paper page
  27. Swamynathan SK, Nambiar A, Guntaka RV: Role of single-stranded DNA regions and Y-box proteins in transcriptional regulation of viral and cellular genes. FASEB J. 1998, 12: 515-522. · DOI
  28. Gasperowicz M, Otto F: Mammalian Groucho homologs: redundancy or specificity?. J Cell Biochem. 2005, 95: 670-687. 10.1002/jcb.20476. · DOI
  29. Hamilton AT, Huntley S, Tran-Gyamfi M, Baggott DM, Gordon L, Stubbs L: Evolutionary expansion and divergence in the ZNF91 subfamily of primate-specific zinc finger genes. Genome Res. 2006, 16: 584-594. 10.1101/gr.4843906. · DOI
  30. Lemons D, McGinnis W: Genomic evolution of Hox gene clusters. Science. 2006, 313: 1918-1922. 10.1126/science.1132040. · DOI · Paper page
  31. Rost B: Twilight zone of protein sequence alignments. Protein Eng. 1999, 12: 85-94. 10.1093/protein/12.2.85. · DOI · Paper page
  32. Liu J, Rost B: Domains, motifs and clusters in the protein universe. Curr Opin Chem Biol. 2003, 7: 5-11. 10.1016/S1367-5931(02)00003-0. · DOI
  33. Li WH, Gu Z, Wang H, Nekrutenko A: Evolutionary analyses of the human genome. Nature. 2001, 409: 847-849. 10.1038/35057039. · DOI
  34. Malumbres M, Barbacid M: Mammalian cyclin-dependent kinases. Trends Biochem Sci. 2005, 30: 630-641. 10.1016/j.tibs.2005.09.005. · DOI · Paper page
  35. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000, 25: 25-29. 10.1038/75556. · DOI · Paper page
  36. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, et al: Initial sequencing and analysis of the human genome. Nature. 2001, 409: 860-921. 10.1038/35057062. · DOI · Paper page
  37. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, et al: The sequence of the human genome. Science. 2001, 291: 1304-1351. 10.1126/science.1058040. · DOI · Paper page
  38. Harrison SC: A structural taxonomy of DNA-binding domains. Nature. 1991, 353: 715-719. 10.1038/353715a0. · DOI · Paper page
  39. Lilley DMJ: DNA-Protein: Structural Interactions. 1995, Oxford: IRL Press at Oxford University Press · DOI
  40. Kummerfeld SK, Teichmann SA: DBD: a transcription factor prediction database. Nucleic Acids Res. 2006, 34: D74-81. 10.1093/nar/gkj131. · DOI
  41. Han J, Gong P, Reddig K, Mitra M, Guo P, Li HS: The fly CAMTA transcription factor potentiates deactivation of rhodopsin, a G protein-coupled light receptor. Cell. 2006, 127: 847-858. 10.1016/j.cell.2006.09.030. · DOI
  42. Finkler A, Ashery-Padan R, Fromm H: CAMTAs: calmodulin-binding transcription activators from plants to human. FEBS Lett. 2007, 581: 3893-3898. 10.1016/j.febslet.2007.07.051. · DOI
  43. Choi MY, Romer AI, Hu M, Lepourcelet M, Mechoor A, Yesilaltay A, Krieger M, Gray PA, Shivdasani RA: A dynamic expression survey identifies transcription factors relevant in mouse digestive tract development. Development. 2006, 133: 4119-4129. 10.1242/dev.02537. · DOI
  44. Kong YM, Macdonald RJ, Wen X, Yang P, Barbera VM, Swift GH: A comprehensive survey of DNA-binding transcription factor gene expression in human fetal and adult organs. Gene Expression Patterns. 2006, 6: 678-686. 10.1016/j.modgep.2006.01.002. · DOI
  45. Coulson RM, Ouzounis CA: The phylogenetic diversity of eukaryotic transcription. Nucleic Acids Res. 2003, 31: 653-660. 10.1093/nar/gkg156. · DOI
  46. Lee AP, Yang Y, Brenner S, Venkatesh B: TFCONES: a database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements. BMC Genomics. 2007, 8: 441-10.1186/1471-2164-8-441. · DOI
  47. Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, Tomoda K, Yamanaka S: Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell. 2007, 131: 861-872. 10.1016/j.cell.2007.11.019. · DOI · Paper page
  48. Roach JC, Smith KD, Strobe KL, Nissen SM, Haudenschild CD, Zhou D, Vasicek TJ, Held GA, Stolovitzky GA, Hood LE, Aderem A: Transcription factor expression in lipopolysaccharide-activated peripheral-blood-derived mononuclear cells. Proc Natl Acad Sci USA. 2007, 104: 16245-16250. 10.1073/pnas.0707757104. · DOI
  49. Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M: The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 2003, 31: 365-370. 10.1093/nar/gkg095. · DOI
  50. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, Copley R, Courcelle E, Das U, Durbin R, Fleischmann W, Gough J, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McDowall J, Mitchell A, Nikolskaya AN, et al: InterPro, progress and status in 2005. Nucleic Acids Res. 2005, 33: D201-205. 10.1093/nar/gki106. · DOI
  51. Sandelin A, Alkema W, Engstrom P, Wasserman WW, Lenhard B: JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 2004, 32: D91-94. 10.1093/nar/gkh012. · DOI
  52. Hubbard T, Andrews D, Caccamo M, Cameron G, Chen Y, Clamp M, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Gilbert J, Hammond M, Herrero J, Hotz H, Howe K, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Kokocinsci F, London D, Longden I, McVicker G, et al: Ensembl 2005. Nucleic Acids Res. 2005, 33: D447-453. 10.1093/nar/gki138. · DOI · Paper page
  53. Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J, Ponting CP, Bork P: SMART 4.0: towards genomic data integration. Nucleic Acids Res. 2004, 32: D142-144. 10.1093/nar/gkh088. · DOI
  54. Krissinel E, Henrick K: Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr. 2004, 60: 2256-2268. 10.1107/S0907444904026460. · DOI
  55. William D, Herbert E: Investigation of proportional link linkage clustering methods. J Classification. 1985, 2: 239-254. 10.1007/BF01908077. · DOI
  56. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-410. · DOI · Paper page
  57. Pruitt KD, Tatusova T, Maglott DR: NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2007, 35: D61-65. 10.1093/nar/gkl842. · DOI · Paper page
  58. Markus Krötzscha DV, Völkelb Max, Hallerb Heiko, Studer Rudi: Semantic Wikipedia. J Web Semantics. 2007, 5: 251-261. · DOI · Paper page
  59. Huntley S, Baggott DM, Hamilton AT, Tran-Gyamfi M, Yang S, Kim J, Gordon L, Branscomb E, Stubbs L: A comprehensive catalog of human KRAB-associated zinc finger genes: insights into the evolutionary history of a large family of transcriptional repressors. Genome Res. 2006, 16: 669-677. 10.1101/gr.4842106. · DOI · Paper page
  60. Ryu T, Jung J, Lee S, Nam HJ, Hong SW, Yoo JW, Lee DK, Lee D: bZIPDB: a database of regulatory information for human bZIP transcription factors. BMC Genomics. 2007, 8: 136-10.1186/1471-2164-8-136. · DOI
  61. Reece-Hoyes JS, Deplancke B, Shingles J, Grove CA, Hope IA, Walhout AJ: A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks. Genome Biol. 2005, 6: R110-10.1186/gb-2005-6-13-r110. · DOI

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Metadata

Authors
Fulton, D. L., Sundararajan, S., Badis, G., Hughes, T. R., Wasserman, W. W., Roach, J. C., & Sladek, R.
Venue
Genome Biology
Publisher
Springer Science and Business Media LLC
Published
2009-03-12
Volume
10
Issue
3
ISSN
1474-760X
DOI
10.1186/gb-2009-10-3-r29
PMC
PMC2691000
Cited by
189
References
3
Language
en
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