CAPER 2.0: An Interactive, Configurable, and Extensible Workflow-Based Platform to Analyze Data Sets from the Chromosome-centric Human Proteome Project

The Chromosome-centric Human Proteome Project (C-HPP) aims to map and annotate the entire human proteome by the “chromosome-by-chromosome” strategy. As the C-HPP proceeds, the increasing volume of proteomic data sets presents a challenge for customized and reproducible bioinformatics data analyses f...

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Bibliographic Details
Published in:Journal of proteome research 2014-01, Vol.13 (1), p.99-106
Main Authors: Wang, Dan, Liu, Zhongyang, Guo, Feifei, Diao, Lihong, Li, Yang, Zhang, Xinlei, Huang, Zechi, Li, Dong, He, Fuchu
Format: Article
Language:English
Subjects:
Chromosomes, Human
Databases, Protein
Genome, Human
Humans
Information Storage and Retrieval
Proteome
Software
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Summary:The Chromosome-centric Human Proteome Project (C-HPP) aims to map and annotate the entire human proteome by the “chromosome-by-chromosome” strategy. As the C-HPP proceeds, the increasing volume of proteomic data sets presents a challenge for customized and reproducible bioinformatics data analyses for mining biological knowledge. To address this challenge, we updated the previous static proteome browser CAPER into a higher version, CAPER 2.0 – an interactive, configurable and extensible workflow-based platform for C-HPP data analyses. In addition to the previous visualization functions of track-view and heatmap-view, CAPER 2.0 presents a powerful toolbox for C-HPP data analyses and also integrates a configurable workflow system that supports the view, construction, edit, run, and share of workflows. These features allow users to easily conduct their own C-HPP proteomic data analyses and visualization by CAPER 2.0. We illustrate the usage of CAPER 2.0 with four specific workflows for finding missing proteins, mapping peptides to chromosomes for genome annotation, integrating peptides with transcription factor binding sites from ENCODE data sets, and functionally annotating proteins. The updated CAPER is available at http://www.bprc.ac.cn/CAPE.
ISSN:1535-3893
1535-3907
DOI:10.1021/pr400795c