TFCONES: A database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements

BMC Genomics

Volumn 8, Issue , 2007, Pages

  Lee, Alison P ^a   Yang, Yuchen ^a   Brenner, Sydney ^a   Venkatesh, Byrappa ^a  

^a INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; MYC PROTEIN; OCTAMER TRANSCRIPTION FACTOR 4; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR SOX2;

ARTICLE; BINDING SITE; CANCER INHIBITION; CELL CYCLE PROGRESSION; CELL DIFFERENTIATION; CELL MATURATION; COMPARATIVE GENOMIC HYBRIDIZATION; DATA BASE; DNA BINDING; DNA FLANKING REGION; GENE CLUSTER; GENE IDENTIFICATION; GENE LOCUS; GENE MAPPING; GENETIC CODE; GENETIC DATABASE; HUMAN; NONHUMAN; PROTEIN PROTEIN INTERACTION; REGULATORY SEQUENCE; TRANSCRIPTION FACTOR GENES AND ASSOCIATED CONSERVED NONCODING ELEMENTS DATABASE; TRANSCRIPTION REGULATION; ANIMAL; GENETICS; INTERNET; VERTEBRATE;

TAKIFUGU; VERTEBRATA;

ANIMALS; DATABASES, GENETIC; HUMANS; INTERNET; TRANSCRIPTION FACTORS; VERTEBRATES;

EID: 37349042272     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-8-441     Document Type: Article

References (47)

1. 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 528918 15489324 10.1101/gr.2584104
2. Kleinjan DA Seawright A Mella S Carr CB Tyas DA Simpson TI Mason JO Price DJ van HV Long-range downstream enhancers are essential for Pax6 expression Dev Biol 2006, 299:563-581 10.1016/j.ydbio.2006.08.060 17014839
3. Flomen RH Vatcheva R Gorman PA Baptista PR Groet J Barisic I Ligutic I Nizetic D Construction and analysis of a sequence-ready map in 4q25: Rieger syndrome can be caused by haploinsufficiency of RIEG, but also by chromosome breaks approximately 90 kb upstream of this gene Genomics 1998, 47:409-413 10.1006/geno.1997.5127 9480756
4. Trembath DG Semina EV Jones DH Patil SR Qian Q Amendt BA Russo AF Murray JC Analysis of two translocation breakpoints and identification of a negative regulatory element in patients with Rieger's syndrome Birth Defects Res A Clin Mol Teratol 2004 70:82-91 10.1002/bdra.10154 14991915
5. Bagheri-Fam S Barrionuevo F Dohrmann U Gunther T Schule R Kemler R Mallo M Kanzler B Scherer G Long-range upstream and downstream enhancers control distinct subsets of the complex spatiotemporal Sox9 expression pattern Dev Biol 2006, 291:382-397 10.1016/j.ydbio.2005.11.013 16458883
6. Bejerano G Pheasant M Makunin I Stephen S Kent WJ Mattick JS Haussler D Ultraconserved elements in the human genome Science 2004 304 1321 1325 10.1126/science.1098119 15131266
7. Pennacchio LA Ahituv N Moses AM Prabhakar S Nobrega MA Shoukry M Minovitsky S Dubchak I Holt A Lewis KD In vivo enhancer analysis of human conserved non-coding sequences Nature 2006, 444:499-502 10.1038/ nature05295 17086198
8. Sandelin A Bailey P Bruce S Engstrom PG Klos JM Wasserman WW Ericson J Lenhard B Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes BMC Genomics 2004, 5:99 544600 15613238 10.1186/1471-2164-5-99
9. Shin JT Priest JR Ovcharenko I Ronco A Moore RK Burns CG MacRae CA Human-zebrafish non-coding conserved elements act in vivo to regulate transcription Nucleic Acids Res 2005, 33:5437-5445 1236720 16179648 10.1093/nar/gki853
10. Woolfe A Goodson M Goode DK Snell P McEwen GK Vavouri T Smith SF North P Callaway H Kelly K Highly conserved non-coding sequences are associated with vertebrate development PLoS Biol 2005, 3:e7 526512 15630479 10.1371/ journal.pbio.0030007
11. Sanges R Kalmar E Claudiani P D'Amato M Muller F Stupka E Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage Genome Biol 2006, 7:R56 1779573 16859531 10.1186/gb-2006-7-7-r56
12. Bray N Dubchak I Pachter L AVID: A global alignment program Genome Res 2003, 13:97-102 430967 12529311 10.1101/gr.789803
13. Frazer KA Elnitski L Church DM Dubchak I Hardison RC Cross-species sequence comparisons: A review of methods and available resources Genome Res 2003, 13:1-12 430969 12529301 10.1101/gr.222003
14. Robertson G Bilenky M Lin K He A Yuen W Dagpinar M Varhol R Teague K Griffith OL Zhang X cisRED: A database system for genome-scale computational discovery of regulatory elements Nucleic Acids Res 2006, 34:D68-D73 1347438 16381958 10.1093/nar/gkj075
15. Sandelin A Wasserman WW Lenhard B ConSite: Web-based prediction of regulatory elements using cross-species comparison Nucleic Acids Res 2004, 32:W249-W252 441510 15215389 10.1093/nar/gkh372
16. Iwama H Gojobori T Highly conserved upstream sequences for transcription factor genes and implications for the regulatory network Proc Natl Acad Sci USA 2004, 101:17156-17161 534610 15572454 10.1073/pnas.0407670101
17. Dieterich C Grossmann S Tanzer A Ropcke S Arndt PF Stadler PF Vingron M Comparative promoter region analysis powered by CORG BMC Genomics 2005, 6:24 555765 15723697 10.1186/1471-2164-6-24
18. Nobrega MA Ovcharenko I Afzal V Rubin EM Scanning human gene deserts for long-range enhancers Science 2003, 302:413 10.1126/science.1088328 14563999
19. Woolfe A Goode DK Cooke J Callaway H Smith S Snell P McEwen GK Elgar G CONDOR: A database resource of developmentally associated conserved non-coding elements BMC Dev Biol 2007, 7:100 2020477 17760977 10.1186/ 1471-213X-7-100
20. Ensembl Genome Browser http://www.ensembl.org
21. Remm M Storm CE Sonnhammer EL Automatic clustering of orthologs and in-paralogs from pairwise species comparisons J Mol Biol 2001, 314:1041-1052 10.1006/jmbi.2000.5197 11743721
22. Christoffels A Koh EG Chia JM Brenner S Aparicio S Venkatesh B Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes Mol Biol Evol 2004, 21:1146-1151 10.1093/molbev/msh114 15014147
23. Felsenstein J PHYLIP (Phylogeny Inference Package) version 3.6. (3.6) Department of Genome Sciences, University of Washington, Seattle 2005
24. RepeatMasker version open-3.1.5 http://www.repeatmasker.org
25. Brudno M Do CB Cooper GM Kim MF Davydov E Green ED Sidow A Batzoglou S LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA Genome Res 2003, 13:721-731 430158 12654723 10.1101/gr.926603
26. Chapman MA Donaldson IJ Gilbert J Grafham D Rogers J Green AR Gottgens B Analysis of multiple genomic sequence alignments: A web resource, online tools, and lessons learned from analysis of mammalian SCL loci Genome Res 2004, 14:313-318 327107 14718377 10.1101/gr.1759004
27. Frazer KA Pachter L Poliakov A Rubin EM Dubchak I VISTA: Computational tools for comparative genomics Nucleic Acids Res 2004, 32:W273-W279 441596 15215394 10.1093/nar/gkh458
28. Loots GG Locksley RM Blankespoor CM Wang ZE Miller W Rubin EM Frazer KA Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons Science 2000, 288:136-140 10.1126/ science.288.5463.136 10753117
29. Beissbarth T Speed TP GOstat: Find statistically overrepresented Gene Ontologies within a group of genes Bioinformatics 2004, 20:1464-1465 10.1093/bioinformatics/bth088 14962934
30. Benjamini Y Hochberg Y Controlling the false discovery rate: A practical and powerful approach to multiple testing Journal of the Royal Statistical Society Series B Methodological 1995, 57:289-300
31. Boyer LA Lee TI Cole MF Johnstone SE Levine SS Zucker JP Guenther MG Kumar RM Murray HL Jenner RG Core transcriptional regulatory circuitry in human embryonic stem cells Cell 2005, 122:947-956 10.1016/ j.cell.2005.08.020 16153702
32. Zeller KI Zhao X Lee CW Chiu KP Yao F Yustein JT Ooi HS Orlov YL Shahab A Yong HC Global mapping of c-Myc binding sites and target gene networks in human B cells Proc Natl Acad Sci USA 2006, 103:17834-17839 1635161 17093053 10.1073/pnas.0604129103
33. Lee TI Jenner RG Boyer LA Guenther MG Levine SS Kumar RM Chevalier B Johnstone SE Cole MF Isono K Control of developmental regulators by Polycomb in human embryonic stem cells Cell 2006, 125:301-313 10.1016/ j.cell.2006.02.043 16630818
34. Transcription Element Search System (TESS) http://www.cbil.upenn.edu/tess
35. The Generic Genome Browser http://www.gmod.org/ggb
36. NCBI WWW Blast web server ftp://ftp.ncbi.nih.gov/blast/executables/
37. Spitz F Gonzalez F Duboule D A global control region defines a chromosomal regulatory landscape containing the HoxD cluster Cell 2003, 113:405-417 10.1016/S0092-8674(03)00310-6 12732147
38. de la Calle-Mustienes E Feijoo CG Manzanares M Tena JJ Rodriguez-Seguel E Letizia A Allende ML Gomez-Skarmeta JL A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts Genome Res 2005, 15:1061-1072 1182218 16024824 10.1101/gr.4004805
39. Goode DK Snell P Smith SF Cooke JE Elgar G Highly conserved regulatory elements around the SHH gene may contribute to the maintenance of conserved synteny across human chromosome 7q36.3 Genomics 2005, 86:172-181 10.1016/j.ygeno.2005.04.006 15939571
40. Lee AP Koh EG Tay A Brenner S Venkatesh B Highly conserved syntenic blocks at the vertebrate Hox loci and conserved regulatory elements within and outside Hox gene clusters Proc Natl Acad Sci USA 2006, 103:6994-6999 1459007 16636282 10.1073/pnas.0601492103
41. Waterston RH Lindblad-Toh K Birney E Rogers J Abril JF Agarwal P Agarwala R Ainscough R Alexandersson M An P Initial sequencing and comparative analysis of the mouse genome Nature 2002, 420:520-562 10.1038/nature01262 12466850
42. Prabhakar S Poulin F Shoukry M Afzal V Rubin EM Couronne O Pennacchio LA Close sequence comparisons are sufficient to identify human cis-regulatory elements Genome Res 2006, 16:855-863 1484452 16769978 10.1101/gr.4717506
43. Cecconi F Proetzel G Alvarez-Bolado G Jay D Gruss P Expression of Meis2, a Knotted-related murine homeobox gene, indicates a role in the differentiation of the forebrain and the somitic mesoderm Dev Dyn 1997, 210:184-190 10.1002/ (SICI)1097-0177(199710)210:2<184::AID-AJA10>3.0.CO;2-E 9337138
44. Capdevila J Tsukui T Rodriquez EC Zappavigna V Izpisua Belmonte JC Control of vertebrate limb outgrowth by the proximal factor Meis2 and distal antagonism of BMPs by Gremlin Mol Cell 1999, 4:839-849 10.1016/ S1097-2765(00)80393-7 10619030
45. Bosse A Zulch A Becker MB Torres M Gomez-Skarmeta JL Modolell J Gruss P Identification of the vertebrate Iroquois homeobox gene family with overlapping expression during early development of the nervous system Mech Dev 1997, 69:169-181 10.1016/S0925-4773(97)00165-2 9486539
46. Fisher S Grice EA Vinton RM Bessling SL McCallion AS Conservation of RET regulatory function from human to zebrafish without sequence similarity Science 2006, 312:276-279 10.1126/science.1124070 16556802
47. Adhikary S Eilers M Transcriptional regulation and transformation by Myc proteins Nat Rev Mol Cell Biol 2005, 6:635-645 10.1038/nrm1703 16064138