TY - JOUR
T1 - ChIP-Array
T2 - Combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor
AU - Qin, Jing
AU - Li, Mulin Jun
AU - Wang, Panwen
AU - Zhang, Michael Q.
AU - Wang, Junwen
N1 - Funding Information:
University Postgraduate Fellowship [to J.Q.] from The University of Hong Kong; Centre for Reproduction Development and Growth of The University of Hong Kong [start up fund to J.W.]; General Research Fund [grant number 778609M to J.W.] from the Research Grants Council of Hong Kong; The National Natural Science Foundation of China and Research Grants Council of Hong Kong Joint Research Scheme [grant number N_HKU752/10 to J.W. and M.Q.Z.]. Funding for open access charge: General Research Fund [grant number 778609M to J.W.] from the Research Grants Council of Hong Kong.
PY - 2011/7/1
Y1 - 2011/7/1
N2 - 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.
AB - 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.
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U2 - 10.1093/nar/gkr332
DO - 10.1093/nar/gkr332
M3 - Article
C2 - 21586587
AN - SCOPUS:79959930131
SN - 0305-1048
VL - 39
SP - W430-W436
JO - Nucleic acids research
JF - Nucleic acids research
IS - SUPPL. 2
ER -