annoPeak: a web application to annotate and visualize peaks from ChIP-seq/ChIP-exo-seq.
CONCLUSIONS
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.


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


BACKGROUND
gustavo.leone@osumc.edu or kun.huang@osumc.edu.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Department of Molecular Virology, Immunology and Medical Genetics College of Medicine, The Ohio State University, Columbus, OH, USA.|Department of Molecular Genetics, College of Biological Sciences, The Ohio State University, Columbus, OH, USA.|Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
Xing
X
Tang
Department of Molecular Virology, Immunology and Medical Genetics College of Medicine, The Ohio State University, Columbus, OH, USA.|Department of Molecular Genetics, College of Biological Sciences, The Ohio State University, Columbus, OH, USA.|Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
Arunima
A
Srivastava
Department of Molecular Virology, Immunology and Medical Genetics College of Medicine, The Ohio State University, Columbus, OH, USA.|Department of Molecular Genetics, College of Biological Sciences, The Ohio State University, Columbus, OH, USA.|Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
Huayang
H
Liu
Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.
Raghu
R
Machiraju
Computer Science and Engineering, The Ohio State University, Columbus, OH, USA.
Kun
K
Huang
Department of Molecular Virology, Immunology and Medical Genetics College of Medicine, The Ohio State University, Columbus, OH, USA.|Department of Molecular Genetics, College of Biological Sciences, The Ohio State University, Columbus, OH, USA.|Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
Gustavo
G
Leone
D000818:Animals; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D004247:DNA / Q000378:metabolism*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D051379:Mice; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*
D014157:Transcription Factors; D004247:DNA