YY1TargetDB: An integral information resource for Yin Yang 1 target loci

Database

Volumn 2013, Issue , 2013, Pages

  Guo, Andy M ^a   Sun, Kun ^a   Su, Xiaoxi ^a   Wang, Huating ^a   Sun, Hao ^a  

^a CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR YY1;

ANIMAL; ARTICLE; CHROMATIN IMMUNOPRECIPITATION; COMPUTER INTERFACE; GENE LOCUS; GENETIC DATABASE; GENETICS; HUMAN; INTERNET; METABOLISM; MOLECULAR GENETICS; MOUSE; PROTEIN BINDING; REPRODUCIBILITY;

ANIMALS; CHROMATIN IMMUNOPRECIPITATION; DATABASES, GENETIC; GENETIC LOCI; HUMANS; INTERNET; MICE; MOLECULAR SEQUENCE ANNOTATION; PROTEIN BINDING; REPRODUCIBILITY OF RESULTS; USER-COMPUTER INTERFACE; YY1 TRANSCRIPTION FACTOR;

MLCS; MLOWN;

EID: 84879377261     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bat007     Document Type: Article

References (25)

1. Gordon,S., Akopyan,G., Garban,H. et al. (2006) Transcription factor YY1: structure, function, and therapeutic implications in cancer biology. Oncogene, 25, 1125-1142.
2. Shi,Y., Lee,J.S. and Galvin,K.M. (1997) Everything you have ever wanted to know about Yin Yang 1. Biochim. Biophys. Acta., 1332, F49-F66.
3. Wang,H., Garzon,R., Sun,H. et al. (2008) NF-kappaB-YY1-miR-29 regulatory circuitry in skeletal myogenesis and rhabdomyosarcoma. Cancer Cell, 14, 369-381.
4. Wang,H., Hertlein,E., Bakkar,N. et al. (2007) NF-kappaB regulation of YY1 inhibits skeletal myogenesis through transcriptional silencing of myofibrillar genes. Mol. Cell. Biol., 27, 4374-4387.
5. Lu,L., Zhou,L., Chen,E.Z. et al. (2012) A Novel YY1-miR-1 regulatory circuit in skeletal myogenesis revealed by genome-wide prediction of YY1-miRNA network. PLoS One, 7, e27596.
6. Zhou,L., Wang,L., Lu,L. et al. (2012) Inhibition of miR-29 by TGF-beta-Smad3 signaling through dual mechanisms promotes transdifferentiation of mouse myoblasts into myofibroblasts. PLoS One, 7, e33766.
7. Lee,H.Y., Chaudhary,J., Walsh,G.L. et al. (1998) Suppression of c-Fos gene transcription with malignant transformation of human bronchial epithelial cells. Oncogene, 16, 3039-3046.
8. Cuddapah,S., Schones,D.E., Cui,K. et al. (2010) Genomic profiling of HMGN1 reveals an association with chromatin at regulatory regions. Mol. Cell. Biol., 31, 700-709.
9. Li,J., Song,J.S., Bell,R.J. et al. (2012) YY1 regulates melanocyte development and function by cooperating with MITF. PLoS Genet., 8, e1002688.
10. Mendenhall,E.M., Koche,R.P., Truong,T. et al. (2010) GC-rich sequence elements recruit PRC2 in mammalian ES cells. PLoS Genet., 6, e1001244.
11. Vella,P., Barozzi,I., Cuomo,A. et al. (2012) Yin Yang 1 extends the Myc-related transcription factors network in embryonic stem cells. Nucleic Acids Res., 40, 3403-3418.
12. Gebhard,C., Benner,C., Ehrich,M. et al. (2010) General transcription factor binding at CpG islands in normal cells correlates with resistance to de novo DNA methylation in cancer cells. Cancer Res., 70, 1398-1407.
13. Rosenbloom,K.R., Dreszer,T.R., Long,J.C. et al. (2012) ENCODE whole-genome data in the UCSC genome browser: update 2012. Nucleic Acids Res., 40, D912-D917.
14. Dunham,I., Kundaje,A., Aldred,S.F. et al . (2012)Anintegrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
15. Li,R., Yu,C., Li,Y. et al. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics, 25, 1966-1967.
16. Feng,J., Liu,T. and Zhang,Y. (2011) Using MACS to identify peaks from ChIP-Seq data. Curr Protoc Bioinformatics, Chapter 2, Unit 2 14.
17. Schones,D.E., Smith,A.D. and Zhang,M.Q. (2007) Statistical significance of cis-regulatory modules. BMC Bioinformatics, 8, 19.
18. Xu,M., Weinberg,C.R., Umbach,D.M. et al. (2011) coMOTIF: a mixture framework for identifying transcription factor and a coregulator motif in ChIP-seq data. Bioinformatics, 27, 2625-2632.
19. Bi,Y., Kim,H., Gupta,R. et al. (2011) Tree-based position weight matrix approach to model transcription factor binding site profiles. PLoS One, 6, e24210.
20. Jin,V.X., Apostolos,J., Nagisetty,N.S. et al. (2009) W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data. Bioinformatics, 25, 3191-3193.
21. Kennedy,B.A., Gao,W., Huang,T.H. et al. (2009) HRTBLDb: an informative data resource for hormone receptors target binding loci. Nucleic Acids Res., 38, D676-D681.
22. Pruitt,K.D., Tatusova,T., Brown,G.R. et al. (2011) NCBI reference sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res., 40, D130-D135.
23. Fujita,P.A., Rhead,B., Zweig,A.S. et al. (2010) The UCSC Genome Browser database: update 2011. Nucleic Acids Res., 39, D876-D882.
24. Ye,J., Zhang,X. and Dong,Z. (1996) Characterization of the human granulocyte-macrophage colony-stimulating factor gene promoter: an AP1 complex and an Sp1-related complex transactivate the promoter activity that is suppressed by a YY1 complex. Mol. Cell. Biol., 16, 157-167.
25. Schlisio,S., Halperin,T., Vidal,M. et al. (2002) Interaction of YY1 with E2Fs, mediated by RYBP, provides a mechanism for specificity of E2F function. EMBO J., 21, 5775-5786.