title: Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data.
abstract: Next-generation sequencing is revolutionizing the identification of transcription factor binding sites throughout the human genome. However, the bioinformatics analysis of large datasets collected using chromatin immunoprecipitation and high-throughput sequencing is often a roadblock that impedes researchers in their attempts to gain biological insights from their experiments. We have developed integrated peak-calling and analysis software (Sole-Search) which is available through a user-friendly interface and (i) converts raw data into a format for visualization on a genome browser, (ii) outputs ranked peak locations using a statistically based method that overcomes the significant problem of false positives, (iii) identifies the gene nearest to each peak, (iv) classifies the location of each peak relative to gene structure, (v) provides information such as the number of binding sites per chromosome and per gene and (vi) allows the user to determine overlap between two different experiments. In addition, the program performs an analysis of amplified and deleted regions of the input genome. This software is web-based and automated, allowing easy and immediate access to all investigators. We demonstrate the utility of our software by collecting, analyzing and comparing ChIP-seq data for six different human transcription factors/cell line combinations.
authors.affiliation: Department of Computer Science, University of California-Davis, Davis, CA 95616, USA.
authors.forename: Kimberly R
authors.initials: KR
authors.lastname: Blahnik
authors.forename: Lei
authors.initials: L
authors.lastname: Dou
authors.forename: Henriette
authors.initials: H
authors.lastname: O'Geen
authors.forename: Timothy
authors.initials: T
authors.lastname: McPhillips
authors.forename: Xiaoqin
authors.initials: X
authors.lastname: Xu
authors.forename: Alina R
authors.initials: AR
authors.lastname: Cao
authors.forename: Sushma
authors.initials: S
authors.lastname: Iyengar
authors.forename: Charles M
authors.initials: CM
authors.lastname: Nicolet
authors.forename: Bertram
authors.initials: B
authors.lastname: Ludäscher
authors.forename: Ian
authors.initials: I
authors.lastname: Korf
authors.forename: Peggy J
authors.initials: PJ
authors.lastname: Farnham
mesh_terms: D001665:Binding Sites; D045744:Cell Line, Tumor; D047369:Chromatin Immunoprecipitation; D050704:E2F4 Transcription Factor / Q000378:metabolism; D005786:Gene Expression Regulation; D006801:Humans; D020407:Internet; D020014:K562 Cells; D050436:Regulatory Elements, Transcriptional; D017422:Sequence Analysis, DNA; D012984:Software; D014157:Transcription Factors / Q000145:classification / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D050704:E2F4 Transcription Factor; D014157:Transcription Factors