EDGEdb: A transcription factor-DNA interaction database for the analysis of C. elegans differential gene expression

BMC Genomics

Volumn 8, Issue , 2007, Pages

  Barrasa, M Inmaculada ^a   Vaglio, Philippe ^b   Cavasino, Fabien ^b   Jacotot, Laurent ^b   Walhout, Albertha J M ^a  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^b Modul Bio   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; TRANSCRIPTION FACTOR;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS DIFFERENTIAL GENE EXPRESSION DATABASE; CONTROLLED STUDY; DIMERIZATION; DNA BINDING; GENE EXPRESSION; GENE EXPRESSION PROFILING; INFORMATION PROCESSING; NONHUMAN; PROTEIN DATABASE; PROTEIN DNA INTERACTION; PROTEIN DOMAIN; SEQUENCE ANALYSIS;

ANIMALS; CAENORHABDITIS ELEGANS; DATABASES, GENETIC; DNA-BINDING PROTEINS; GENE REGULATORY NETWORKS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REGULATORY SEQUENCES, NUCLEIC ACID; TRANSCRIPTION FACTORS;

CAENORHABDITIS ELEGANS;

EID: 33846994717     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-8-21     Document Type: Article

References (27)

1. Blais A Dynlacht BD Constructing transcriptional regulatory networks. Genes Dev 2005 19 1499-1511 10.1101/gad.1325605 15998805
2. Walhout AJM Unraveling Transcription Regulatory Networks by Protein-DNA and Protein-Protein Interaction Mapping. Genome Res 2006 16 1445-1454 10.1101/gr.5321506 17053092
3. Deplancke B Dupuy D Vidal M Walhout AJM A Gateway-compatible yeast one-hybrid system Genome Res 2004 14 2093-2101 528925 15489331 10.1101/ gr.2445504
4. Deplancke B Vermeirssen V Arda HE Martinez NJ Walhout AJM Gateway-compatible yeast one-hybrid screens. CSH Protocols 2006 doi:10.1101/pdb.prot4590
5. Deplancke B Mukhopadhyay A Ao W Elewa AM Grove CA Martinez NJ Sequerra R Doucette-Stam L Reece-Hoyes JS Hope IA Tissenbaum HA Mango SE Walhout AJM A gene-centered C. elegans protein-DNA interaction network. Cell 2006 125 1193-1205 10.1016/j.cell.2006.04.038 16777607
6. Vermeirssen V Barrasa MI Hidalgo C Babon JAB Sequerra R Doucette-Stam L Barabasi AL Walhout AJM Transcription Factor Modularity in a Gene-Centered C. elegans Core Neuronal Protein-DNA Interaction Network submitted 2007
7. Vermeirssen V A C. elegans transcription factor resource for smart pooling-based yeast one -and two-hybrid assays. in preparation
8. Li S Armstrong CM Bertin N Ge H Milstein S Boxem M Vidalain PO Han JDJ Chesneau A Hao T Goldberg DS Li N Martinez M Rual JF Lamesch P Xu L Tewari M Wong SL Zhang LV Berriz GF Jacotot L Vaglio P Reboul J Hirozane-Kishikawa T Li Q Gabel HW Elewa A Bauemgartner B Rose DJ Yu H Bosak S Sequerra R Fraser A Mango SE Saxton WM Strome S van den Heuvel S Piano F Vandenhaute J Sardet C Gerstein M Doucette-Stam L Gunsalus K Harper JW Cusick ME Roth FP Hill D Vidal M A map of the interactome network of the metazoan C. elegans. Science 2004 303 540-543 1698949 14704431 10.1126/science.1091403
9. Rual JF Venkatesan K Hao T Hirozane-Kishikawa T Dricot A Li N Berriz GF Gibbons FD Dreze M Ayivi-Guedehoussou N Klitgord N Simon C Boxem M Milstein S Rosenberg J Goldberg DS Zhang LV Wong SL Franklin G Li S Albala JS Lim J Fraughton C Llamosas E Cevik S Bex C Lamesch P Sikorski RS Vandenhaute J Zoghbi HY Smolyar A Bosak S Sequerra R Doucette-Stamm L Cusick ME Hill DE Roth FP Vidal M Towards a proteome-scale map of the human protein-protein interaction network Nature 2005 437 1173-1178 10.1038/nature04209 16189514
10. Giot L Bader JS Brouwer C Chaudhuri A Kuang B Li Y Hao YL Ooi CE Godwin B Vitols E Vijayadamodar G Pochart P Machineni H Welsh M Kong Y Zerhusen B Malcolm R Varrone Z Collis A Minto M Burgess S McDaniel L Stimpson E Spriggs F Williams J Neurath K Ioime N Agee M Voss E Furtak K Renzulli R Aanensen N Carrolla S Bickelhaupt E Lazovatsky Y DaSilva A Zhong J Stanyon CA Finley RL Jr. White KP Braverman M Jarvie T Gold S Leach M Knight J Shimkets RA McKenna MP Chant J Rothberg JM A protein interaction map of Drosophila melanogaster Science 2003 302 1727-1736 10.1126/science.1090289 14605208
11. Schwarz EM Antoshechkin I Bastiani C Bieri T Blasiar D Canaran P Chan J Chen N Chen WJ Davis P Fiedler TJ Girard L Harris TW Kenny EE Kishore R Lawson D Lee R Muller HM Nakamura C Ozersky P Petcherski A Rogers A Spooner W Tuli MA Van Auken K Wang D Durbin R Spieth J Stein LD Sternberg PW WormBase: Better software, richer content Nucleic Acids Res 2006 34 D475-8 1347424 16381915 10.1093/nar/gkj061
12. Wormbase http://www.wormbase.org
13. Matys V Kel-Margoulis OV Fricke E Liebich I Land S Barre-Dirrie A Reuter I Chekmenev D Krull M Hornischer K Voss N Stegmaier P Lewicki-Potapov B Saxel H Kel AE Wingender E TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes Nucleic Acids Res 2006 34 D108-10 1347505 16381825 10.1093/nar/gkj143
14. Transfac http://www.gene-regulation.com
15. Vlieghe D Sandelin A De Bleser PJ Vleminckx K Wasserman WW van Roy F Lenhard B A new generation of JASPAR, the open-access repository for transcription factor binding site profiles Nucleic Acids Res 2006 34 D95-7 1347477 16381983 10.1093/nar/gkj115
16. Jaspar http://www.jaspar.cgb.ki.se
17. Montgomery SB Griffith OL Sleumer MC Bergman CM Bilenky M Pleasance ED Prychyna Y Zhang X Jones SJ ORegAnno: An open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation Bioinformatics 2006 22 637-640 10.1093/bioinformatics/btk027 16397004
18. oreganno http://www.oreganno.org
19. Reece-Hoyes JS Deplancke B Shingles J Grove CA Hope IA Walhout AJM A compendium of C. elegans regulatory transcription factors: A resource for mapping transcription regulatory networks. Genome Biol 2005 6 R110 1414109 16420670 10.1186/gb-2005-6-13-r110
20. Bioperl http://www.bioperl.org
21. E chromosomes ftp://ftp.sanger.ac.uk/pub/wormbase/development_release/ CHROMOSOMES
22. EG IDs ftp://ftp.wormbase.org/pub/worbase/genomes/elegans/annotations/ gene_IDs/current.gz
23. Gbrowse http://www.gmod.org
24. Stein LD Mungall C Shu S Caudy M Mangone M Day A Nickerson E Stajich JE Harris TW Arva A Lewis S The generic genome browser: A building block for a model organism system database Genome Res 2002 12 1599-1610 187535 12368253 10.1101/gr.403602
25. Worfdb http://worfdb.dfci.harvard.edu
26. Vaglio P Lamesch P Reboul J Rual JF Martinez M Hill D Vidal M WorfDB: the Caenorhabditis elegans ORFeome Database Nucleic Acids Res 2003 31 237-240 165539 12519990 10.1093/nar/gkg092
27. Wormbook http://www.wormbook.org/