title: Systematic discovery of cofactor motifs from ChIP-seq data by SIOMICS.
abstract: Understanding transcriptional regulatory elements and particularly the transcription factor binding sites represents a significant challenge in computational biology. The chromatin immunoprecipitation followed by massive parallel sequencing (ChIP-seq) experiments provide an unprecedented opportunity to study transcription factor binding sites on the genome-wide scale. Here we describe a recently developed tool, SIOMICS, to systematically discover motifs and binding sites of transcription factors and their cofactors from ChIP-seq data. Unlike other tools, SIOMICS explores the co-binding properties of multiple transcription factors in short regions to predict motifs and binding sites. We have previously shown that the original SIOMICS method predicts motifs and binding sites of more cofactors in more accurate and time-effective ways than two popular methods. In this paper, we present the extended SIOMICS method, SIOMICS_Extension, and demonstrate its usage for systematic discovery of cofactor motifs and binding sites. The SIOMICS tool, including SIOMICS and SIOMICS_Extension, are available at http://hulab.ucf.edu/research/projects/SIOMICS/SIOMICS.html.
authors.affiliation: Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816, USA. Electronic address: jding@cs.ucf.edu.
authors.forename: Jun
authors.initials: J
authors.lastname: Ding
authors.affiliation: Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL 32816, USA. Electronic address: dhillonv10@knights.ucf.edu.
authors.forename: Vikram
authors.initials: V
authors.lastname: Dhillon
authors.affiliation: Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL 32816, USA. Electronic address: xiaoman@mail.ucf.edu.
authors.forename: Xiaoman
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816, USA. Electronic address: haihu@cs.ucf.edu.
authors.forename: Haiyan
authors.initials: H
authors.lastname: Hu
mesh_terms: D001665:Binding Sites; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry; D005786:Gene Expression Regulation; D050436:Regulatory Elements, Transcriptional
chemical_list: D004247:DNA
keywords: ChIP-seq; Cofactor; Motif; SIOMICS; Transcription factor; Transcription factor binding sites