Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules

Genome Sequences ◽

Regulatory Modules ◽

Erroneous attribution of relevant transcription factor binding sites despite successful prediction of cis-regulatory modules

BMC Genomics ◽

10.1186/1471-2164-12-578 ◽

2011 ◽

Vol 12 (1) ◽

Cited By ~ 12

Author(s):

Marc S Halfon ◽

Qianqian Zhu ◽

Elizabeth R Brennan ◽

Yiyun Zhou

Keyword(s):

Transcription Factor ◽

Binding Sites ◽

Regulatory Modules ◽

Factor Binding ◽

Successful Prediction

REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila

Nucleic Acids Research ◽

10.1093/nar/gkm876 ◽

2007 ◽

Vol 36 (Database) ◽

pp. D594-D598 ◽

Cited By ~ 58

Author(s):

M. S. Halfon ◽

S. M. Gallo ◽

C. M. Bergman

Keyword(s):

Transcription Factor ◽

Binding Sites ◽

Regulatory Modules ◽

Conserved sections of the transcription regulatory modules in Drosophila early genes, including homotypic transcription factor-binding sites, are arranged with an 84-nt period, which corresponds to the superhelical turn length of nucleosomal DNA

BIOPHYSICS ◽

10.1134/s0006350916010139 ◽

2016 ◽

Vol 61 (1) ◽

pp. 43-46 ◽

Cited By ~ 1

Author(s):

A. P. Lifanov ◽

V. J. Makeev ◽

N. G. Esipova

Keyword(s):

Transcription Factor ◽

Binding Sites ◽

Regulatory Modules ◽

Factor Binding ◽

Early Genes ◽

Nucleosomal Dna ◽

Superhelical Turn

Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules

BMC Bioinformatics ◽

10.1186/s12859-016-1354-5 ◽

2016 ◽

Vol 17 (1) ◽

Author(s):

Natalia Acevedo-Luna ◽

Leonardo Mariño-Ramírez ◽

Armand Halbert ◽

Ulla Hansen ◽

David Landsman ◽

...

Keyword(s):

Transcription Factor ◽

Transcription Start Site ◽

Binding Sites ◽

Start Site ◽

Transcription Start ◽

Regulatory Modules ◽

Factor Binding ◽

Positional Conservation

Faculty Opinions recommendation of Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1017662.206496 ◽

2004 ◽

Author(s):

Carlos F Barbas

Keyword(s):

Transcription Factor ◽

Binding Sites ◽

Noncoding Rnas ◽

Human Chromosomes ◽

Faculty Opinions recommendation of Position specific variation in the rate of evolution in transcription factor binding sites.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1022543.258615 ◽

2004 ◽

Author(s):

Emmanouil Dermitzakis

Keyword(s):

Transcription Factor ◽

Binding Sites ◽

Factor Binding ◽

Rate Of Evolution ◽

Specific Variation

Faculty Opinions recommendation of Divergence of transcription factor binding sites across related yeast species.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1089279.548953 ◽

2007 ◽

Author(s):

Emmanouil Dermitzakis

Keyword(s):

Transcription Factor ◽

Binding Sites ◽

Yeast Species ◽

Faculty Opinions recommendation of Genome-wide inference of natural selection on human transcription factor binding sites.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718018456.793479473 ◽

2013 ◽

Author(s):

Peter Keightley

Keyword(s):

Transcription Factor ◽

Natural Selection ◽

Binding Sites ◽

Factor Binding ◽

Genome Wide ◽

Human Transcription Factor

Gene Variants and Haplotypes Modifying Transcription Factor Binding Sites in the Human Cyclooxygenase 1 and 2 (PTGS1 and PTGS2) Genes

Current Drug Metabolism ◽

10.2174/138920021502140327180336 ◽

2014 ◽

Vol 15 (2) ◽

pp. 182-195 ◽

Cited By ~ 13

Author(s):

Jose Agundez ◽

David Gonzalez-Alvarez ◽

Miguel Vega-Rodriguez ◽

Emilia Botello ◽

Elena Garcia-Martin

Keyword(s):

Transcription Factor ◽

Binding Sites ◽

Gene Variants ◽

Factor Binding ◽

Cyclooxygenase 1

Structure-Based Ab Initio Prediction of Transcription Factor–Binding Sites

Methods in Molecular Biology - Computational Systems Biology ◽

10.1007/978-1-59745-243-4_2 ◽

2009 ◽

pp. 23-41 ◽

Cited By ~ 8

Author(s):

L. Angela Liu ◽

Joel S. Bader

Keyword(s):

Transcription Factor ◽

Ab Initio ◽

Binding Sites ◽

Factor Binding ◽

Ab Initio Prediction