DWE: discriminating word enumerator

Bioinformatics
Pavel SumazinMichael Q Zhang

Abstract

Tissue-specific transcription factor binding sites give insight into tissue-specific transcription regulation. We describe a word-counting-based tool for de novo tissue-specific transcription factor binding site discovery using expression information in addition to sequence information. We incorporate tissue-specific gene expression through gene classification to positive expression and repressed expression. We present a direct statistical approach to find overrepresented transcription factor binding sites in a foreground promoter sequence set against a background promoter sequence set. Our approach naturally extends to synergistic transcription factor binding site search. We find putative transcription factor binding sites that are overrepresented in the proximal promoters of liver-specific genes relative to proximal promoters of liver-independent genes. Our results indicate that binding sites for hepatocyte nuclear factors (especially HNF-1 and HNF-4) and CCAAT/enhancer-binding protein (C/EBPbeta) are the most overrepresented in proximal promoters of liver-specific genes. Our results suggest that HNF-4 has strong synergistic relationships with HNF-1, HNF-4 and HNF-3beta and with C/EBPbeta. Programs are available for use over ...Continue Reading

References

May 1, 1991·Proceedings of the National Academy of Sciences of the United States of America·K G XanthopoulosJ E Darnell
Apr 1, 1990·Computer Applications in the Biosciences : CABIOS·G Z HertzG D Stormo
Jan 1, 1984·Bulletin of Mathematical Biology·M S WatermanD J Galas
Jan 1, 1994·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·R KnüppelE Wingender
Feb 21, 1998·Nucleic Acids Research·R Cavin PérierP Bucher
Mar 29, 2000·Nucleic Acids Research·J van HeldenJ Collado-Vides
Feb 15, 2001·Nature Genetics·H J BussemakerE D Siggia
Dec 26, 2001·Nucleic Acids Research·Yutaka SuzukiSumio Sugano
Dec 20, 2002·Nucleic Acids Research·Saurabh Sinha, Martin Tompa
Dec 31, 2002·Molecular Cell·Pantelis Hatzis, Iannis Talianidis
Aug 26, 2003·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Saurabh Sinha
Apr 16, 2004·Cell·Michael A Beer, Saeed Tavazoie

❮ Previous
Next ❯

Citations

Apr 1, 2009·Physiology and Molecular Biology of Plants : an International Journal of Functional Plant Biology·Ravi Ramesh PathakNandula Raghuram
Feb 6, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Leping Li
Mar 15, 2008·EURASIP Journal on Bioinformatics & Systems Biology·Arvind RaoJames Douglas Engel
Oct 2, 2007·BMC Bioinformatics·Michael Q Zhang
Nov 17, 2009·PLoS Computational Biology·Eivind ValenAnders Krogh
Aug 23, 2012·PloS One·Shisong MaSavithramma P Dinesh-Kumar
Feb 22, 2014·BMC Systems Biology·Jialiang YangXiu-Feng Wan
Mar 24, 2009·Briefings in Bioinformatics·Huajun ChenJake Y Chen
Jun 10, 2009·Methods : a Companion to Methods in Enzymology·Christina S Barr
Sep 17, 2016·Nature Communications·John A LeesJukka Corander
Jun 10, 2006·Briefings in Bioinformatics·Alexander Yu Mitrophanov, Mark Borodovsky

❮ Previous
Next ❯

Related Concepts

Related Feeds

CREs: Gene & Cell Therapy

Gene and cell therapy advances have shown promising outcomes for several diseases. The role of cis-regulatory elements (CREs) is crucial in the design of gene therapy vectors. Here is the latest research on CREs in gene and cell therapy.

© 2021 Meta ULC. All rights reserved