ConTra v2: a tool to identify transcription factor binding sites across species, update 2011

被引：45

作者：

Broos, Stefan ^{[1
]}

Hulpiau, Paco

Galle, Jeroen

Hooghe, Bart

Van Roy, Frans

De Bleser, Pieter

机构：

[1] Univ Ghent, VIB, Dept Mol Biomed Res, B-9000 Ghent, Belgium

来源：

NUCLEIC ACIDS RESEARCH | 2011年 / 39卷

关键词：

GENE-REGULATION; IDENTIFICATION; MICRORNAS; PROMOTER; EXPRESSION; INTRON; CELLS; RNAS;

D O I：

10.1093/nar/gkr355

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Transcription factors are important gene regulators with distinctive roles in development, cell signaling and cell cycling, and they have been associated with many diseases. The ConTra v2 web server allows easy visualization and exploration of predicted transcription factor binding sites in any genomic region surrounding coding or non-coding genes. In this new version, users can choose from nine reference organisms ranging from human to yeast. ConTra v2 can analyze promoter regions, 5'-UTRs, 3'-UTRs and introns or any other genomic region of interest. Hundreds of position weight matrices are available to choose from, but the user can also upload any other matrices for detecting specific binding sites. A typical analysis is run in four simple steps of choosing the gene, the transcript, the region of interest and then selecting one or more transcription factor binding sites. The ConTra v2 web server is freely available at http://bioit.dmbr.ugent.be/contrav2/index.php.

引用

页码：W74 / W78

页数：5

共 21 条

[1] Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences [J].

Berger, Michael F. ;

Badis, Gwenael ;

Gehrke, Andrew R. ;

Talukder, Shaheynoor ;

Philippakis, Anthony A. ;

Pena-Castillo, Lourdes ;

Alleyne, Trevis M. ;

Mnaimneh, Sanie ;

Botvinnik, Olga B. ;

Chan, Esther T. ;

Khalid, Faiqua ;

Zhang, Wen ;

Newburger, Daniel ;

Jaeger, Savina A. ;

Morris, Quaid D. ;

Bulyk, Martha L. ;

Hughes, Timothy R. .

CELL, 2008, 133 (07) :1266-1276

[2] Aligning multiple genomic sequences with the threaded blockset aligner [J].

Blanchette, M ;

Kent, WJ ;

Riemer, C ;

Elnitski, L ;

Smit, AFA ;

Roskin, KM ;

Baertsch, R ;

Rosenbloom, K ;

Clawson, H ;

Green, ED ;

Haussler, D ;

Miller, W .

GENOME RESEARCH, 2004, 14 (04) :708-715

[3] Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs [J].

Cawley, S ;

Bekiranov, S ;

Ng, HH ;

Kapranov, P ;

Sekinger, EA ;

Kampa, D ;

Piccolboni, A ;

Sementchenko, V ;

Cheng, J ;

Williams, AJ ;

Wheeler, R ;

Wong, B ;

Drenkow, J ;

Yamanaka, M ;

Patel, S ;

Brubaker, S ;

Tammana, H ;

Helt, G ;

Struhl, K ;

Gingeras, TR .

CELL, 2004, 116 (04) :499-509

[4] Insights from genomic profiling of transcription factors [J].

Farnham, Peggy J. .

NATURE REVIEWS GENETICS, 2009, 10 (09) :605-616

[5] Most mammalian mRNAs are conserved targets of microRNAs [J].

Friedman, Robin C. ;

Farh, Kyle Kai-How ;

Burge, Christopher B. ;

Bartel, David P. .

GENOME RESEARCH, 2009, 19 (01) :92-105

[6] Genomic Targets of the KRAB and SCAN Domain-containing Zinc Finger Protein 263 [J].

Frietze, Seth ;

Lan, Xun ;

Jin, Victor X. ;

Farnham, Peggy J. .

JOURNAL OF BIOLOGICAL CHEMISTRY, 2010, 285 (02) :1393-1403

[7] An evolutionarily conserved mechanism for microRNA-223 expression revealed by microRNA gene profiling [J].

Fukao, Taro ;

Fukuda, Yoko ;

Kiga, Kotaro ;

Sharif, Jafar ;

Hino, Kimihiro ;

Enomoto, Yutaka ;

Kawamura, Aya ;

Nakamura, Kaito ;

Takeuchi, Tsutomu ;

Tanabe, Masanobu .

CELL, 2007, 129 (03) :617-631

[8] The TEA Transcription Factor Tec1 Confers Promoter-Specific Gene Regulation by Ste12-Dependent and -Independent Mechanisms [J].

Heise, Barbara ;

van der Felden, Julia ;

Kern, Sandra ;

Malcher, Mario ;

Brueckner, Stefan ;

Moesch, Hans-Ulrich .

EUKARYOTIC CELL, 2010, 9 (04) :514-531

[9] Gene regulation by transcription factors and microRNAs [J].

Hobert, Oliver .

SCIENCE, 2008, 319 (5871) :1785-1786

[10] ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species [J].

Hooghe, Bart ;

Hulpiau, Paco ;

van Roy, Frans ;

De Bleser, Pieter .

NUCLEIC ACIDS RESEARCH, 2008, 36 :W128-W132

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