title: Cistrome: an integrative platform for transcriptional regulation studies.
abstract: The increasing volume of ChIP-chip and ChIP-seq data being generated creates a challenge for standard, integrative and reproducible bioinformatics data analysis platforms. We developed a web-based application called Cistrome, based on the Galaxy open source framework. In addition to the standard Galaxy functions, Cistrome has 29 ChIP-chip- and ChIP-seq-specific tools in three major categories, from preliminary peak calling and correlation analyses to downstream genome feature association, gene expression analyses, and motif discovery. Cistrome is available at http://cistrome.org/ap/.
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA.
authors.forename: Tao
authors.initials: T
authors.lastname: Liu
authors.forename: Jorge A
authors.initials: JA
authors.lastname: Ortiz
authors.forename: Len
authors.initials: L
authors.lastname: Taing
authors.forename: Clifford A
authors.initials: CA
authors.lastname: Meyer
authors.forename: Bernett
authors.initials: B
authors.lastname: Lee
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.forename: Hyunjin
authors.initials: H
authors.lastname: Shin
authors.forename: Swee S
authors.initials: SS
authors.lastname: Wong
authors.forename: Jian
authors.initials: J
authors.lastname: Ma
authors.forename: Ying
authors.initials: Y
authors.lastname: Lei
authors.forename: Utz J
authors.initials: UJ
authors.lastname: Pape
authors.forename: Michael
authors.initials: M
authors.lastname: Poidinger
authors.forename: Yiwen
authors.initials: Y
authors.lastname: Chen
authors.forename: Kevin
authors.initials: K
authors.lastname: Yeung
authors.forename: Myles
authors.initials: M
authors.lastname: Brown
authors.forename: Yaron
authors.initials: Y
authors.lastname: Turpaz
authors.forename: X Shirley
authors.initials: XS
authors.lastname: Liu
mesh_terms: D047369:Chromatin Immunoprecipitation / Q000379:methods*; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D005786:Gene Expression Regulation; D006801:Humans; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D012984:Software; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
chemical_list: D014157:Transcription Factors