title: ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor.
abstract: Chromatin immunoprecipitation (ChIP) coupled with high-throughput techniques (ChIP-X), such as next generation sequencing (ChIP-Seq) and microarray (ChIP-chip), has been successfully used to map active transcription factor binding sites (TFBS) of a transcription factor (TF). The targeted genes can be activated or suppressed by the TF, or are unresponsive to the TF. Microarray technology has been used to measure the actual expression changes of thousands of genes under the perturbation of a TF, but is unable to determine if the affected genes are direct or indirect targets of the TF. Furthermore, both ChIP-X and microarray methods produce a large number of false positives. Combining microarray expression profiling and ChIP-X data allows more effective TFBS analysis for studying the function of a TF. However, current web servers only provide tools to analyze either ChIP-X or expression data, but not both. Here, we present ChIP-Array, a web server that integrates ChIP-X and expression data from human, mouse, yeast, fruit fly and Arabidopsis. This server will assist biologists to detect direct and indirect target genes regulated by a TF of interest and to aid in the functional characterization of the TF. ChIP-Array is available at http://jjwanglab.hku.hk/ChIP-Array, with free access to academic users.
authors.affiliation: Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong SAR, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Qin
authors.forename: Mulin Jun
authors.initials: MJ
authors.lastname: Li
authors.forename: Panwen
authors.initials: P
authors.lastname: Wang
authors.forename: Michael Q
authors.initials: MQ
authors.lastname: Zhang
authors.forename: Junwen
authors.initials: J
authors.lastname: Wang
mesh_terms: D000818:Animals; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis; D050436:Regulatory Elements, Transcriptional; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors