ChIP-Array

ChIP-Array is a web server that integrates ChIP-X and expression data from human, mouse, yeast, fruit fly, and Arabidopsis. This tool has been developed to assist biologists in detecting both direct and indirect target genes regulated by the transcription factor (TF) of interest, as well as to aid in the functional characterization of the TF.

The chromatin immunoprecipitation technique coupled with high-throughput techniques such as next-generation sequencing (ChIP-Seq) and microarray (ChIP-chip) have been successfully used to map active transcription factor binding sites (TFBS) of a transcription factor (TF). However, microarray technology has been used to measure the actual expression changes of thousands of genes under the perturbation of a TF, but it is limited in determining whether the affected genes are direct or indirect targets of the TF.

ChIP-X and microarray methods often produce many false positives. To address this issue, combining microarray expression profiling and ChIP-X data allows more effective TFBS analysis for studying the function of a TF. However, most web servers currently only provide tools to analyze ChIP-X or expression data, but not both.

This web server fills the gap and provides a comprehensive analysis of both types of data, allowing researchers to study the function of a TF more effectively. With ChIP-Array, biologists can access a wide range of tools to analyze ChIP-X and expression data together, enabling them to detect direct and indirect target genes regulated by the TF of interest.