scholarly journals Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences

2008 ◽  
Vol 24 (13) ◽  
pp. i165-i171 ◽  
Author(s):  
Lucas D. Ward ◽  
Harmen J. Bussemaker
Keyword(s):  
Transcription Factor ◽  
Transcription Factor Binding ◽  
Promoter Sequences ◽  
Factor Binding ◽  
Alignment Free ◽  
Orthologous Promoter ◽  
Functional Transcription Factor

scholarly journals Genomic Promoter Analysis Predicts Functional Transcription Factor Binding

2008 ◽  
Vol 2008 ◽  
pp. 1-9 ◽  
Author(s):  
J. Sunil Rao ◽  
Suresh Karanam ◽  
Colleen D. McCabe ◽  
Carlos S. Moreno
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Proximal Promoter ◽  
Marginal Effect ◽  
Promoter Sequences ◽  
Factor Binding ◽  
Functional Transcription Factor

Background. The computational identification of functional transcription factor binding sites (TFBSs) remains a major challenge of computational biology. Results. We have analyzed the conserved promoter sequences for the complete set of human RefSeq genes using our conserved transcription factor binding site (CONFAC) software. CONFAC identified 16296 human-mouse ortholog gene pairs, and of those pairs, 9107 genes contained conserved TFBS in the 3 kb proximal promoter and first intron. To attempt to predict in vivo occupancy of transcription factor binding sites, we developed a novel marginal effect isolator algorithm that builds upon Bayesian methods for multigroup TFBS filtering and predicted the in vivo occupancy of two transcription factors with an overall accuracy of 84%. Conclusion. Our analyses show that integration of chromatin immunoprecipitation data with conserved TFBS analysis can be used to generate accurate predictions of functional TFBS. They also show that TFBS cooccurrence can be used to predict transcription factor binding to promoters in vivo.

scholarly journals ConBind: motif-aware cross-species alignment for the identification of functional transcription factor binding sites

2015 ◽  
Vol 44 (8) ◽  
pp. e72-e72 ◽  
Author(s):  
Stefan H. Lelieveld ◽  
Judith Schütte ◽  
Maurits J.J. Dijkstra ◽  
Punto Bawono ◽  
Sarah J. Kinston ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Factor Binding ◽  
Functional Transcription Factor

scholarly journals Large-scale turnover of functional transcription factor binding sites in Drosophila

2005 ◽  
Vol preprint (2006) ◽  
pp. e130
Author(s):  
Alan M. Moses ◽  
Daniel Pollard ◽  
David A Nix ◽  
Venky N. Iyer ◽  
Xiao-Yong Li ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Large Scale ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Factor Binding ◽  
Functional Transcription Factor

Transcriptional activity and Sp 1/3 transcription factor binding to the P1 promoter sequences of the human AβH-J-J locus

FEBS Journal ◽  
2007 ◽  
Vol 274 (17) ◽  
pp. 4476-4490 ◽  
Author(s):  
Giordana Feriotto ◽  
Alessia Finotti ◽  
Giulia Breveglieri ◽  
Susan Treves ◽  
Francesco Zorzato ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcriptional Activity ◽  
Transcription Factor Binding ◽  
Promoter Sequences ◽  
Factor Binding
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