CisOrtho: A program pipeline for genome-wide identification of transcription factor target using phylogenetic footprinting

BMC Bioinformatics

Volumn 5, Issue , 2004, Pages

  Bigelow, Henry R ^a   Wenick, Adam S ^a   Wong, Allan ^a   Hobert, Oliver ^a  

^a The New York Presbyterian Hospital   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CAENORHABDITIS; CAENORHABDITIS ELEGANS; DNA-BINDING SPECIFICITY; FOOTPRINTING; HOMEODOMAIN TRANSCRIPTION FACTOR; POTENTIAL SITES; TARGET GENES; WEIGHT MATRICES;

CONSERVATION; PIPELINES; TRANSCRIPTION FACTORS;

GENES;

DNA; HOMEODOMAIN PROTEIN; TRANSCRIPTION FACTOR; HELMINTH DNA; SPACER DNA;

ARTICLE; BINDING SITE; CAENORHABDITIS; CAENORHABDITIS BRIGGSAE; CAENORHABDITIS ELEGANS; COMPUTER PROGRAM; CONTROLLED STUDY; DNA BINDING; DNA FOOTPRINTING; GENE FUNCTION; GENE IDENTIFICATION; GENE TARGETING; GENETIC CODE; GENETIC CONSERVATION; MOLECULAR PHYLOGENY; NONHUMAN; ANIMAL; BIOLOGY; GENE; GENETIC DATABASE; GENETICS; GENOME; INTERNET; PHYLOGENY; PROCEDURES; SEQUENCE HOMOLOGY;

CAENORHABDITIS; CAENORHABDITIS BRIGGSAE; CAENORHABDITIS ELEGANS; NEMATODA;

ANIMALS; CAENORHABDITIS; CAENORHABDITIS ELEGANS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA FOOTPRINTING; DNA, HELMINTH; DNA, INTERGENIC; GENES, HELMINTH; GENOME; INTERNET; PHYLOGENY; SEQUENCE HOMOLOGY, NUCLEIC ACID; SOFTWARE; SOFTWARE DESIGN; SOFTWARE VALIDATION; TRANSCRIPTION FACTORS;

EID: 2942521105     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-5-27     Document Type: Article

References (18)

1. Bulyk ML: Computational prediction of transcription-factor binding site locations. Genome Biol 2003, 5:201.
2. Sosinsky A, Bonin CP, Mann RS, Honig B: Target Explorer: An automated tool for the identification of new target genes for a specified set of transcription factors. Nucleic Acids Res 2003, 31:3589-3592.
3. Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, Rubin GM, Eisen MB: Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci U S A 2002, 99:757-762.
4. Tronche F, Ringeisen F, Blumenfeld M, Yaniv M, Pontoglio M: Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome. J Mol Biol 1997, 266:231-245.
5. Tagle DA, Koop BF, Goodman M, Slightom JL, Hess DL, Jones RT: Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. J Mol Biol 1988, 203:439-455.
6. Cliften PF, Hillier LW, Fulton L, Graves T, Miner T, Gish WR, Waterston RH, Johnston M: Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res 2001, 11:1175-1186.
7. Wasserman WW, Palumbo M, Thompson W, Fickett JW, Lawrence CE: Human-mouse genome comparisons to locate regulatory sites. Nat Genet 2000, 26:225-228.
8. Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES: Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 2003, 423:241-254.
9. GuhaThakurta D, Palomar L, Stormo GD, Tedesco P, Johnson TE, Walker DW, Lithgow G, Kim S, Link CD: Identification of a novel cis-regulatory element involved in the heat shock response in Caenorhabditis elegans using microarray gene expression and computational methods. Genome Res 2002, 12:701-712.
10. Loots GG, Ovcharenko I, Pachter L, Dubchak I, Rubin EM: rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res 2002, 12:832-839.
11. Webb CT, Shabalina SA, Ogurtsov AY, Kondrashov AS: Analysis of similarity within 142 pairs of orthologous intergenic regions of Caenorhabditis elegans and Caenorhabditis briggsae. Nucleic Acids Res 2002, 30:1233-1239.
12. McGuire AM, Hughes JD, Church GM: Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. Genome Res 2000, 10:744-757.
13. Levy S, Hannenhalli S, Workman C: Enrichment of regulatory signals in conserved non-coding genomic sequence. Bioinformatics 2001, 17:871-877.
14. The-C.elegans-Sequencing-Consortium: Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 1998, 282:2012-2018.
15. Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D'Eustachio P, Fitch DH, Fulton LA, Fulton RE, Griffiths-Jones S, Harris TW, Hillier LW, Kamath R, Kuwabara PE, Mardis ER, Marra MA, Miner TL, Minx P, Mullikin JC, Plumb RW, Rogers J, Schein JE, Sohrmann M, Spieth J, Stajich JE, Wei C, Willey D, Wilson RK, Durbin R, Waterston RH: The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics. PLoS Biol 2003, 1:E45.
16. Altun-Gultekin Z, Andachi Y, Tsalik EL, Pilgrim D, Kohara Y, Hobert O: A regulatory cascade of three homeobox genes, ceh-10, ttx-3 and ceh-23, controls cell fate specification of a defined interneuron class in C. elegans. Development 2001, 128:1951-1969.
17. Eddy SR: Profile hidden Markov models. Bioinformatics 1998, 14:755-763.
18. Conkright MD, Guzman E, Flechner L, Su AI, Hogenesch JB, Montminy M: Genome-wide analysis of CREB target genes reveals a core promoter requirement for cAMP responsiveness. Mol Cell 2003, 11:1101-1108.