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.
Article
CAS
PubMed Central
PubMed
Google Scholar
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.
Article
CAS
PubMed Central
PubMed
Google Scholar
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.
Article
CAS
PubMed
Google Scholar
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.
Article
CAS
PubMed
Google Scholar
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.
Article
CAS
PubMed
Google Scholar
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.
Article
CAS
PubMed
Google Scholar
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.
Article
CAS
PubMed
Google Scholar
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: 99-10.1186/1471-2164-5-99.
Article
PubMed Central
PubMed
Google Scholar
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. 10.1093/nar/gki853.
Article
CAS
PubMed Central
PubMed
Google Scholar
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: e7-10.1371/journal.pbio.0030007.
Article
PubMed Central
PubMed
Google Scholar
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: R56-10.1186/gb-2006-7-7-r56.
Article
PubMed Central
PubMed
Google Scholar
Bray N, Dubchak I, Pachter L: AVID: A global alignment program. Genome Res. 2003, 13: 97-102. 10.1101/gr.789803.
Article
CAS
PubMed Central
PubMed
Google Scholar
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. 10.1101/gr.222003.
Article
CAS
PubMed Central
PubMed
Google Scholar
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. 10.1093/nar/gkj075.
Article
CAS
PubMed Central
PubMed
Google Scholar
Sandelin A, Wasserman WW, Lenhard B: ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Res. 2004, 32: W249-W252. 10.1093/nar/gkh372.
Article
CAS
PubMed Central
PubMed
Google Scholar
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. 10.1073/pnas.0407670101.
Article
CAS
PubMed Central
PubMed
Google Scholar
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: 24-10.1186/1471-2164-6-24.
Article
PubMed Central
PubMed
Google Scholar
Nobrega MA, Ovcharenko I, Afzal V, Rubin EM: Scanning human gene deserts for long-range enhancers. Science. 2003, 302: 413-10.1126/science.1088328.
Article
CAS
PubMed
Google Scholar
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: 100-10.1186/1471-213X-7-100.
Article
PubMed Central
PubMed
Google Scholar
Ensembl Genome Browser. [http://www.ensembl.org]
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.
Article
CAS
PubMed
Google Scholar
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.
Article
CAS
PubMed
Google Scholar
Felsenstein J: PHYLIP (Phylogeny Inference Package) version 3.6. (3.6). 2005, Department of Genome Sciences, University of Washington, Seattle
Google Scholar
RepeatMasker version open-3.1.5. [http://www.repeatmasker.org]
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. 10.1101/gr.926603.
Article
CAS
PubMed Central
PubMed
Google Scholar
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. 10.1101/gr.1759004.
Article
CAS
PubMed Central
PubMed
Google Scholar
Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I: VISTA: computational tools for comparative genomics. Nucleic Acids Res. 2004, 32: W273-W279. 10.1093/nar/gkh458.
Article
CAS
PubMed Central
PubMed
Google Scholar
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.
Article
CAS
PubMed
Google Scholar
Beissbarth T, Speed TP: GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics. 2004, 20: 1464-1465. 10.1093/bioinformatics/bth088.
Article
CAS
PubMed
Google Scholar
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.
Google Scholar
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.
Article
CAS
PubMed Central
PubMed
Google Scholar
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. 10.1073/pnas.0604129103.
Article
CAS
PubMed Central
PubMed
Google Scholar
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.
Article
CAS
PubMed Central
PubMed
Google Scholar
Transcription Element Search System (TESS). [http://www.cbil.upenn.edu/tess]
The Generic Genome Browser. [http://www.gmod.org/ggb]
NCBI WWW Blast web server. [ftp://ftp.ncbi.nih.gov/blast/executables/]
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.
Article
CAS
PubMed
Google Scholar
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. 10.1101/gr.4004805.
Article
CAS
PubMed Central
PubMed
Google Scholar
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.
Article
CAS
PubMed
Google Scholar
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. 10.1073/pnas.0601492103.
Article
CAS
PubMed Central
PubMed
Google Scholar
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.
Article
CAS
PubMed
Google Scholar
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. 10.1101/gr.4717506.
Article
CAS
PubMed Central
PubMed
Google Scholar
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.
Article
CAS
PubMed
Google Scholar
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.
Article
CAS
PubMed
Google Scholar
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.
Article
CAS
PubMed
Google Scholar
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.
Article
CAS
PubMed
Google Scholar
Adhikary S, Eilers M: Transcriptional regulation and transformation by Myc proteins. Nat Rev Mol Cell Biol. 2005, 6: 635-645. 10.1038/nrm1703.
Article
CAS
PubMed
Google Scholar