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AnnoPeak: a Web Application to Annotate and Visualize Peaks from ChIP-seq/ChIP-exo-seq

Overview
Journal Bioinformatics
Publisher Oxford University Press
Specialty Biology
Date 2017 Feb 8
PMID 28169395
Citations 4
Authors
Xing Tang
Arunima Srivastava
Huayang Liu
Raghu Machiraju
Kun Huang
Gustavo Leone
Affiliations
Soon will be listed here.
Abstract

Summary: We developed annoPeak, a web application to annotate, visualize and compare predicted protein-binding regions derived from ChIP-seq/ChIP-exo-seq experiments using human and mouse cells. Users can upload peak regions from multiple experiments onto the annoPeak server to annotate them with biological context, identify associated target genes and categorize binding sites with respect to gene structure. Users can also compare multiple binding profiles intuitively with the help of visualization tools and tables provided by annoPeak. In general, annoPeak will help users identify patterns of genome wide transcription factor binding profiles, assess binding profiles in different biological contexts and generate new hypotheses.

Availability And Implementation: The web service is freely accessible through URL: http://ccc-annopeak.osumc.edu/annoPeak . Source code is available at https://github.com/XingTang2014/annoPeak .

Contact: gustavo.leone@osumc.edu or kun.huang@osumc.edu.

Supplementary Information: Supplementary data are available at Bioinformatics online.

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References
1.
Culhane A, Schwarzl T, Sultana R, Picard K, Picard S, Lu T . GeneSigDB--a curated database of gene expression signatures. Nucleic Acids Res. 2009; 38(Database issue):D716-25. PMC: 2808880. DOI: 10.1093/nar/gkp1015. View
2.
Lee B, Iyer V . Genome-wide studies of CCCTC-binding factor (CTCF) and cohesin provide insight into chromatin structure and regulation. J Biol Chem. 2012; 287(37):30906-13. PMC: 3438923. DOI: 10.1074/jbc.R111.324962. View
3.
Chen H, Tsai S, Leone G . Emerging roles of E2Fs in cancer: an exit from cell cycle control. Nat Rev Cancer. 2009; 9(11):785-97. PMC: 3616489. DOI: 10.1038/nrc2696. View
4.
Heinz S, Benner C, Spann N, Bertolino E, Lin Y, Laslo P . Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010; 38(4):576-89. PMC: 2898526. DOI: 10.1016/j.molcel.2010.05.004. View
5.
Rosenbloom K, Sloan C, Malladi V, Dreszer T, Learned K, Kirkup V . ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res. 2012; 41(Database issue):D56-63. PMC: 3531152. DOI: 10.1093/nar/gks1172. View