Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data.

BMC Bioinformatics
Ravi GuptaRamana V Davuluri

Abstract

Use of alternative gene promoters that drive widespread cell-type, tissue-type or developmental gene regulation in mammalian genomes is a common phenomenon. Chromatin immunoprecipitation methods coupled with DNA microarray (ChIP-chip) or massive parallel sequencing (ChIP-seq) are enabling genome-wide identification of active promoters in different cellular conditions using antibodies against Pol-II. However, these methods produce enrichment not only near the gene promoters but also inside the genes and other genomic regions due to the non-specificity of the antibodies used in ChIP. Further, the use of these methods is limited by their high cost and strong dependence on cellular type and context. We trained and tested different state-of-art ensemble and meta classification methods for identification of Pol-II enriched promoter and Pol-II enriched non-promoter sequences, each of length 500 bp. The classification models were trained and tested on a bench-mark dataset, using a set of 39 different feature variables that are based on chromatin modification signatures and various DNA sequence features. The best performing model was applied on seven published ChIP-seq Pol-II datasets to provide genome wide annotation of mouse gene prom...Continue Reading

References

Jan 1, 1990·Biopolymers·P S HoL B Clark
Jun 1, 1986·Proceedings of the National Academy of Sciences of the United States of America·K J BreslauerL A Marky
Oct 20, 1986·Journal of Molecular Biology·S C SatchwellA A Travers
Mar 17, 1995·Journal of Molecular Biology·A A GorinW K Olson
May 31, 1996·Journal of Molecular Biology·M A el Hassan, C R Calladine
Jul 3, 1998·Nucleic Acids Research·R D Blake, S G Delcourt
Sep 16, 1998·Proceedings of the National Academy of Sciences of the United States of America·W K OlsonV B Zhurkin
Jun 15, 1999·Bioinformatics·R D BlakeJ SantaLucia
Jan 7, 2000·Journal of Molecular Biology·M J PackerC A Hunter
Jan 7, 2000·Journal of Molecular Biology·M J PackerC A Hunter
Mar 5, 2002·Genome Research·Thomas A Down, Tim J P Hubbard
Nov 6, 2004·Nature Biotechnology·Vladimir B BajicSumio Sugano
Jul 1, 2005·Nature·Tae Hoon KimBing Ren
Sep 22, 2006·IEEE Transactions on Pattern Analysis and Machine Intelligence·Juan J RodríguezCarlos J Alonso
Jul 3, 2007·Nature·Tarjei S MikkelsenBradley E Bernstein
Nov 10, 2007·Nucleic Acids Research·Sam Griffiths-JonesAnton J Enright
Dec 13, 2007·Genome Biology·J Ramon GoñiModesto Orozco
Dec 22, 2007·Genome Research·Thomas AbeelYves Van de Peer
Mar 11, 2008·Trends in Genetics : TIG·Ramana V DavuluriTim H-M Huang
Mar 11, 2008·Cell·Dustin E SchonesKeji Zhao
May 30, 2008·Nature·Tarjei S MikkelsenAlexander Meissner
Jul 5, 2008·Nature·Alexander MeissnerEric S Lander
Nov 11, 2008·Genome Research·Xiaowo WangMichael Q Zhang
Jan 6, 2009·Nature Biotechnology·Joel RozowskyMark B Gerstein
May 30, 2009·Bioinformatics·Thomas AbeelYvan Saeys
Jul 23, 2009·Journal of Cellular Biochemistry·Benjamin M Lee, Louis C Mahadevan

❮ Previous
Next ❯

Citations

Sep 17, 2010·Nucleic Acids Research·Hao SunRamana V Davuluri
Dec 14, 2011·Nucleic Acids Research·Marco A Mendoza-ParraHinrich Gronemeyer
Nov 21, 2012·BMC Genomics·Cenny TaslimTim Hui-Ming Huang
Feb 13, 2013·BMC Medical Genomics·Guohua WangYadong Wang
Aug 30, 2013·Kidney International·Imari MimuraMasaomi Nangaku
Aug 23, 2012·Pharmacology & Therapeutics·Sharmistha PalRamana V Davuluri
Jan 1, 2011·Wiley Interdisciplinary Reviews. Data Mining and Knowledge Discovery·Xiang ChenHeping Zhang
Apr 26, 2013·Molecular BioSystems·Beena M Kadakkuzha, Sathyanarayanan V Puthanveettil
Oct 2, 2019·Cold Spring Harbor Perspectives in Medicine·Andrea Forman, Jilliane Sotelo
Mar 14, 2021·Science Immunology·Tim D HolmesYenan T Bryceson

❮ Previous
Next ❯

Methods Mentioned

BETA
immunoprecipitation
ChIP-seq

Software Mentioned

CoreBoost
Forest
FirstEF
Random
UCSC genome browser
ProSOM
MPromDb
Eponine
EP3
HM

Related Concepts

Related Feeds

Bioinformatics in Biomedicine

Bioinformatics in biomedicine incorporates computer science, biology, chemistry, medicine, mathematics and statistics. Discover the latest research on bioinformatics in biomedicine here.