TY - JOUR
T1 - EpiRegNet
T2 - Constructing epigenetic regulatory network from high throughput gene expression data for humans
AU - Wang, Lily Yan
AU - Wang, Panwen
AU - Li, Mulin Jun
AU - Qin, Jing
AU - Wang, Xiaowo
AU - Zhang, Michael Q.
AU - Wang, Junwen
N1 - Funding Information:
We thank Sam Bevan for editing the manuscript. The project was supported by University Postgraduate Fellowships (to L.Y.W. and J.Q.) from the University of Hong Kong, the Research Grants Council of Hong Kong (N_HKU752/10, 781511M, 778609M, AoE M04/04), and Food and Health Bureau of Hong Kong (10091262).
PY - 2011
Y1 - 2011
N2 - The advances of high throughput profiling methods, such as microarray gene profiling and RNA-seq, have enabled researchers to identify thousands of differentially expressed genes under a certain perturbation. Much work has been done to understand the genetic factors that contribute to the expression changes by searching the overrepresented regulatory motifs in the promoter regions of these genes. However, the changes could also be caused by epigenetic regulation, especially histone modifications, and no web server has been constructed to study the epigenetic factors responsible for gene expression changes. Here, we present a web tool for this purpose. Provided with different categories of genes (e.g., upregulated, downregulated or unchanged genes), the server will find epigenetic factors responsible for the difference among the categories and construct an epigenetic regulatory network. Furthermore, it will perform colocalization analyses between these epigenetic factors and transcription factors, which were collected from large scale experimental ChIP-seq or computational predicted data. In addition, for users who want to analyze dynamic change of a histone modification mark under different cell conditions, the server will find direct and indirect target genes of this mark by integrative analysis of experimental data and computational prediction, and present a regulatory network around this mark. Both networks can be visualized by a user friendly interface and the data are downloadable in batch. The server currently supports 12 cell types in human, including ESC and CD4+ T cells, and will expand as more public data are available. It also allows user to create a self-defined cell type, upload and analyze multiple ChIP-seq data. It is freely available to academic users at http://jjwanglab.org/EpiRegNet.
AB - The advances of high throughput profiling methods, such as microarray gene profiling and RNA-seq, have enabled researchers to identify thousands of differentially expressed genes under a certain perturbation. Much work has been done to understand the genetic factors that contribute to the expression changes by searching the overrepresented regulatory motifs in the promoter regions of these genes. However, the changes could also be caused by epigenetic regulation, especially histone modifications, and no web server has been constructed to study the epigenetic factors responsible for gene expression changes. Here, we present a web tool for this purpose. Provided with different categories of genes (e.g., upregulated, downregulated or unchanged genes), the server will find epigenetic factors responsible for the difference among the categories and construct an epigenetic regulatory network. Furthermore, it will perform colocalization analyses between these epigenetic factors and transcription factors, which were collected from large scale experimental ChIP-seq or computational predicted data. In addition, for users who want to analyze dynamic change of a histone modification mark under different cell conditions, the server will find direct and indirect target genes of this mark by integrative analysis of experimental data and computational prediction, and present a regulatory network around this mark. Both networks can be visualized by a user friendly interface and the data are downloadable in batch. The server currently supports 12 cell types in human, including ESC and CD4+ T cells, and will expand as more public data are available. It also allows user to create a self-defined cell type, upload and analyze multiple ChIP-seq data. It is freely available to academic users at http://jjwanglab.org/EpiRegNet.
KW - Epigenetics
KW - Gene regulation
KW - Histone modification
KW - Microarray
KW - Network
KW - RNA-seq
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UR - http://www.scopus.com/inward/citedby.url?scp=83255166557&partnerID=8YFLogxK
U2 - 10.4161/epi.6.12.18176
DO - 10.4161/epi.6.12.18176
M3 - Article
C2 - 22139581
AN - SCOPUS:83255166557
SN - 1559-2294
VL - 6
SP - 1505
EP - 1512
JO - Epigenetics
JF - Epigenetics
IS - 12
ER -