Motif enrichment tool

Nucleic Acids Research

Volumn 42, Issue W1, 2014, Pages

  Blatti, Charles ^a   Sinha, Saurabh ^a,b  

^a Department of Computer Science University of Illinois at Urbana Champaign ^*  (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ARTICLE; CHROMATIN IMMUNOPRECIPITATION; COMPUTER INTERFACE; DNA BINDING; MOTIF ENRICHMENT TOOL; ONLINE SYSTEM; PREDICTION; PRIORITY JOURNAL; PROTEIN MOTIF; TRANSCRIPTION REGULATION; WEB BROWSER;

ANIMALS; BINDING SITES; DNA; HUMANS; INTERNET; MICE; NUCLEOTIDE MOTIFS; REGULATORY ELEMENTS, TRANSCRIPTIONAL; SEQUENCE ANALYSIS, DNA; SOFTWARE; TRANSCRIPTION FACTORS;

MAGNOLIOPHYTA; METAZOA; PLANARIA;

EID: 84904821294     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku456     Document Type: Article

References (24)

1. Patil,M.A., Chua,M.S., Pan,K.H., Lin,R., Lih,C.J., Cheung,S.T., Ho,C., Li,R., Fan,S.T., Cohen,S.N. et al. (2005) An integrated data analysis approach to characterize genes highly expressed in hepatocellular carcinoma. Oncogene, 24, 3737-3747.
2. Ashburner,M., Ball,C.A., Blake,J.A., Botstein,D., Butler,H., Cherry,J.M., Davis,A.P., Dolinski,K., Dwight,S.S., Eppig,J.T. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
3. Huang da,W., Sherman,B.T. and Lempicki,R.A. (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protoc., 4, 44-57.
4. Huang da,W., Sherman,B.T. and Lempicki,R.A. (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res., 37, 1-13.
5. Bailey,T.L., Boden,M., Buske,F.A., Frith,M., Grant,C.E., Clementi,L., Ren,J., Li,W.W. and Noble,W.S. (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res., 37, W202-W208.
6. Wenger,A.M., Clarke,S.L., Guturu,H., Chen,J., Schaar,B.T., McLean,C.Y. and Bejerano,G. (2013) PRISM offers a comprehensive genomic approach to transcription factor function prediction. Genome Res., 23, 889-904.
7. Warren,W.C., Clayton,D.F., Ellegren,H., Arnold,A.P., Hillier,L.W., Kunstner,A., Searle,S., White,S., Vilella,A.J., Fairley,S. et al. (2010) The genome of a songbird. Nature, 464, 757-762.
8. Ament,S.A., Blatti,C.A., Alaux,C., Wheeler,M.M., Toth,A.L., Le Conte,Y., Hunt,G.J., Guzman-Novoa,E., Degrandi-Hoffman,G., Uribe-Rubio,J.L. et al. (2012) New meta-analysis tools reveal common transcriptional regulatory basis for multiple determinants of behavior. Proc. Natl. Acad. Sci. U.S.A., 109, E1801-E1810.
9. Kim,J., Cunningham,R., James,B., Wyder,S., Gibson,J.D., Niehuis,O., Zdobnov,E.M., Robertson,H.M., Robinson,G.E., Werren,J.H. et al. (2010) Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances. PLoS Comput. Biol., 6, e1000652.
10. Herrmann,C., Van de Sande,B., Potier,D. and Aerts,S. (2012) i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules. Nucleic Acids Res., 40, e114.
11. Negre,N., Brown,C.D.,Ma,L., Bristow,C.A., Miller,S.W.,Wagner,U., Kheradpour,P., Eaton,M.L., Loriaux,P., Sealfon,R. et al. (2011) A cis-regulatory map of the Drosophila genome. Nature, 471, 527-531.
12. Sinha,S., van Nimwegen,E. and Siggia,E.D. (2003) A probabilistic method to detect regulatory modules. Bioinformatics, 19(Suppl.1), i292-301.
13. Portales-Casamar,E., Thongjuea,S., Kwon,A.T., Arenillas,D., Zhao,X., Valen,E., Yusuf,D., Lenhard,B.,Wasserman,W.W. and Sandelin,A. (2010) JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res., 38, D105-D110.
14. Matys,V., Fricke,E., Geffers,R., Gossling,E., Haubrock,M., Hehl,R., Hornischer,K., Karas,D., Kel,A.E., Kel-Margoulis,O.V. et al. (2003) TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res., 31, 374-378.
15. Jolma,A., Yan,J., Whitington,T., Toivonen,J., Nitta,K.R., Rastas,P., Morgunova,E., Enge,M., Taipale,M., Wei,G. et al. (2013) DNA-binding specificities of human transcription factors. Cell, 152, 327-339.
16. Zhu,L.J., Christensen,R.G., Kazemian,M., Hull,C.J., Enuameh,M.S., Basciotta,M.D., Brasefield,J.A., Zhu,C., Asriyan,Y., Lapointe,D.S. et al. (2011) FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system. Nucleic Acids Res., 39, D111-D117.
17. Franco-Zorrilla,J.M., Lopez-Vidriero,I., Carrasco,J.L., Godoy,M., Vera,P. and Solano,R. (2014) DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc. Natl. Acad. Sci. U.S.A., 111, 2367-2372.
18. Kazemian,M., Blatti,C., Richards,A., McCutchan,M., Wakabayashi-Ito,N., Hammonds,A.S., Celniker,S.E., Kumar,S., Wolfe,S.A., Brodsky,M.H. et al. (2010) Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials. PLoS Biol., 8, epublish.
19. Thomas,S., Li,X.Y., Sabo,P.J., Sandstrom,R., Thurman,R.E., Canfield,T.K., Giste,E., Fisher,W., Hammonds,A., Celniker,S.E. et al. (2011) Dynamic reprogramming of chromatin accessibility during Drosophila embryo development. Genome Biol., 12, R43.
20. Rosenbloom,K.R., Sloan,C.A., Malladi,V.S., Dreszer,T.R., Learned,K., Kirkup,V.M.,Wong,M.C., Maddren,M., Fang,R., Heitner,S.G. et al. (2013) ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res., 41, D56-D63.
21. Kasprzyk,A. (2011) BioMart: driving a paradigm change in biological data management. Database, 2011, bar049.
22. Kazemian,M., Brodsky,M.H. and Sinha,S. (2011) Genome Surveyor 2.0: cis-regulatory analysis in Drosophila. Nucleic Acids Res., 39, W79-W85.
23. Tomancak,P., Berman,B.P., Beaton,A., Weiszmann,R., Kwan,E., Hartenstein,V., Celniker,S.E. and Rubin,G.M. (2007) Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biol., 8, R145.
24. Hahm,K., Sum,E.Y., Fujiwara,Y., Lindeman,G.J., Visvader,J.E. and Orkin,S.H. (2004) Defective neural tube closure and anteroposterior patterning in mice lacking the LIM protein LMO4 or its interacting partner Deaf-1. Mol. Cell. Biol., 24, 2074-2082.