| |
bZIPDB : A database of regulatory information for human bZIP transcription factors
- 作者:Taewoo Ryu (1)
Juhyun Jung (1) Sunjae Lee (1) Ho Jung Nam (1) Sun Woo Hong (2) Jae Wook Yoo (2) Dong-ki Lee (2) Doheon Lee (1)
- 刊名:BMC Genomics
- 出版年:2007
- 出版时间:December 2007
- 年:2007
- 卷:8
- 期:1
- 全文大小:956KB
- 参考文献:1. Cowell IG, Skinner A, Hurst HC: class="a-plus-plus">Transcriptional repression by a novel member of the bZIP family of transcription factors. / Mol Cell Biol 1992, class="a-plus-plus">12:3070鈥?077.
2. Rinehart-Kim J, Johnston M, Birrer M, Bos T: class="a-plus-plus">Alterations in the gene expression profile of MCF-7 breast tumor cells in response to c-Jun. / Int J Cancer 2000, class="a-plus-plus">88:180鈥?90. class="external" href="http://dx.doi.org/10.1002/1097-0215(20001015)88:2<180::AID-IJC6>3.0.CO;2-H">CrossRef 3. Petrovick MS, Hiebert SW, Friedman AD, Hetherington CJ, Tenen DG, Zhang DE: class="a-plus-plus">Multiple functional domains of AML1: PU.1 and C/EBPalpha synergize with different regions of AML1. / Mol Cell Biol 1998, class="a-plus-plus">18:3915鈥?925. 4. Cammenga J, Mulloy JC, Berguido FJ, MacGrogan D, Viale A, Nimer SD: class="a-plus-plus">Induction of C/EBPalpha activity alters gene expression and differentiation of human CD34+ cells. / Blood 2003, class="a-plus-plus">101:2206鈥?214. class="external" href="http://dx.doi.org/10.1182/blood-2002-05-1546">CrossRef 5. Newman JR, Keating AE: class="a-plus-plus">Comprehensive Identification of Human bZIP Interactions with Coiled-Coil Arrays. / Science 2003, class="a-plus-plus">300:2097鈥?101. class="external" href="http://dx.doi.org/10.1126/science.1084648">CrossRef 6. Hayakawa J, Mittal S, Wang Y, Korkmaz KS, Adamson E, English C, Ohmichi M, McClelland M, Mercola D: class="a-plus-plus">Identification of promoters bound by c-Jun/ATF2 during rapid large-scale gene activation following genotoxic stress. / Mol Cell 2004, class="a-plus-plus">16:521鈥?35. class="external" href="http://dx.doi.org/10.1016/j.molcel.2004.10.024">CrossRef 7. Coxon A, Rozenblum E, Park YS, Joshi N, Tsurutani J, Dennis PA, Kirsch IR, Kaye FJ: class="a-plus-plus">Mect1-Maml2 fusion oncogene linked to the aberrant activation of cyclic AMP/CREB regulated genes. / Cancer Res 2005, class="a-plus-plus">65:7137鈥?144. class="external" href="http://dx.doi.org/10.1158/0008-5472.CAN-05-1125">CrossRef 8. Peri S, Navarro JD, Kristiansen TZ, Amanchy R, Surendranath V, Muthusamy B, Gandhi TK, Chandrika KN, Deshpande N, Suresh S, Rashmi BP, Shanker K, Padma N, Niranjan V, Harsha HC, Talreja N, Vrushabendra BM, Ramya MA, Yatish AJ, Joy M, Shivashankar HN, Kavitha MP, Menezes M, Choudhury DR, Ghosh N, Saravana R, Chandran S, Mohan S, Jonnalagadda CK, Prasad CK, Kumar-Sinha C, Deshpande KS, Pandey A: class="a-plus-plus">Human protein reference database as a discovery resource for proteomics. / Nucleic Acids Res 2004, class="a-plus-plus">32:D497鈥?01. class="external" href="http://dx.doi.org/10.1093/nar/gkh070">CrossRef 9. Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos DU, Land S, Lewicki-Potapov B, Michael H, Munch R, Reuter I, Rotert S, Saxel H, Scheer M, Thiele S, Wingender E: class="a-plus-plus">TRANSFAC: transcriptional regulation, from patterns to profiles. / Nucleic Acids Res 2003, class="a-plus-plus">31:374鈥?78. class="external" href="http://dx.doi.org/10.1093/nar/gkg108">CrossRef 10. class="a-plus-plus">Entrez PubMed [class="a-plus-plus">http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed] 11. Walker WH, Sanborn BM, Habener JF: class="a-plus-plus">An isoform of transcription factor CREM expressed during spermatogenesis lacks the phosphorylation domain and represses cAMP-induced transcription. / Proc Natl Acad Sci 1994, class="a-plus-plus">91:12423鈥?2427. class="external" href="http://dx.doi.org/10.1073/pnas.91.26.12423">CrossRef 12. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D: class="a-plus-plus">The Database of Interacting Proteins: 2004 update. / Nucleic Acids Res 2004, class="a-plus-plus">32:D449鈥?51. class="external" href="http://dx.doi.org/10.1093/nar/gkh086">CrossRef 13. Hughes JD, Estep PW, Tavazoie S, Church GM: class="a-plus-plus">Computational identification of cis-regulatory elements associated with groups of functionally related genes in class="a-plus-plus">Saccharomyces cerevisiae class="a-plus-plus">. / J Mol Biol 2000, class="a-plus-plus">296:1205鈥?214. class="external" href="http://dx.doi.org/10.1006/jmbi.2000.3519">CrossRef 14. Beer MA, Tavazoie S: class="a-plus-plus">Predicting gene expression from sequence. / Cell 2004, class="a-plus-plus">117:185鈥?98. class="external" href="http://dx.doi.org/10.1016/S0092-8674(04)00304-6">CrossRef 15. Maglott D, Ostell J, Pruitt KD, Tatusova T: class="a-plus-plus">Entrez Gene: gene-centered information at NCBI. / Nucleic Acids Res 2005, class="a-plus-plus">33:D54鈥?8. class="external" href="http://dx.doi.org/10.1093/nar/gki031">CrossRef 16. Consortium GO: class="a-plus-plus">The Gene Ontology (GO) project in 2006. / Nucleic Acids Res 2006, class="a-plus-plus">34:D322鈥?26. class="external" href="http://dx.doi.org/10.1093/nar/gkj021">CrossRef 17. class="a-plus-plus">HUGO Gene Nomenclature Committee [class="a-plus-plus">http://www.gene.ucl.ac.uk/nomenclature/] 18. class="a-plus-plus">Cytoscape [class="a-plus-plus">http://www.cytoscape.org/] 19. Wasserman WW, Palumbo M, Thompson W, Fickett JW, Lawrence CE: class="a-plus-plus">Human-mouse genome comparisons to locate regulatory sites. / Nat Genet 2000, class="a-plus-plus">26:225鈥?28. class="external" href="http://dx.doi.org/10.1038/79965">CrossRef 20. Jegga AG, Gupta A, Gowrisankar S, Deshmukh MA, Connolly S, Finley K, Aronow BJ: class="a-plus-plus">CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes. / Nucleic Acids Res 2005, class="a-plus-plus">33:W408鈥?11. class="external" href="http://dx.doi.org/10.1093/nar/gki486">CrossRef 21. class="a-plus-plus">Gene Expression Omnibus [class="a-plus-plus">http://www.ncbi.nlm.nih.gov/geo/] 22. Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R: class="a-plus-plus">The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. / Nat Biotechnol 2004, class="a-plus-plus">22:177鈥?83. class="external" href="http://dx.doi.org/10.1038/nbt926">CrossRef
- 作者单位:Taewoo Ryu (1)
Juhyun Jung (1) Sunjae Lee (1) Ho Jung Nam (1) Sun Woo Hong (2) Jae Wook Yoo (2) Dong-ki Lee (2) Doheon Lee (1)
1. Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejeon, 305-701, Korea 2. Department of Chemistry, Pohang University of Science and Technology, Hyo-ja-dong, Nam-gu, Pohang, 790-784, Korea
文摘
Background Basic region-leucine zipper (bZIP) proteins are a class of transcription factors (TFs) that play diverse roles in eukaryotes. Malfunctions in these proteins lead to cancer and various other diseases. For detailed characterization of these TFs, further public resources are required. Description We constructed a database, designated bZIPDB, containing information on 49 human bZIP TFs, by means of automated literature collection and manual curation. bZIPDB aims to provide public data required for deciphering the gene regulatory network of the human bZIP family, e.g., evaluation or reference information for the identification of regulatory modules. The resources provided by bZIPDB include (1) protein interaction data including direct binding, phosphorylation and functional associations between bZIP TFs and other cellular proteins, along with other types of interactions, (2) bZIP TF-target gene relationships, (3) the cellular network of bZIP TFs in particular cell lines, and (4) gene information and ontology. In the current version of the database, 721 protein interactions and 560 TF-target gene relationships are recorded. bZIPDB is annually updated for the newly discovered information. Conclusion bZIPDB is a repository of detailed regulatory information for human bZIP TFs that is collected and processed from the literature, designed to facilitate analysis of this protein family. bZIPDB is available for public use at http://biosoft.kaist.ac.kr/bzipdb.
| |
NGLC 2004-2010.National Geological Library of China All Rights Reserved.
Add:29 Xueyuan Rd,Haidian District,Beijing,PRC. Mail Add: 8324 mailbox 100083
For exchange or info please contact us via email.
| |