CAPER: a Chromosome-Assembled human Proteome browsER

被引：20

作者：

Guo, Feifei ^{[1
,2
,3
,4
]}

Wang, Dan ^{[4
]}

Liu, Zhongyang ^{[4
]}

Lu, Liang ^{[4
]}

Zhang, Wei ^{[4
,5
]}

Sun, Haiyan ^{[4
,6
]}

Zhang, Hongxing ^{[4
]}

Ma, Jie ^{[4
]}

Wu, Songfeng ^{[4
]}

Li, Ning ^{[4
]}

Jiang, Ying ^{[4
]}

Zhu, Weimin ^{[4
]}

Qin, Jun ^{[4
]}

Xu, Ping ^{[4
]}

Li, Dong ^{[4
]}

He, Fuchu ^{[1
,2
,3
,4
]}

机构：

[1] Peking Union Med Coll, Inst Basic Med Sci, Beijing 100005, Peoples R China

[2] Peking Union Med Coll, Sch Basic Med, Beijing 100005, Peoples R China

[3] Chinese Acad Med Sci, Beijing 100005, Peoples R China

[4] Beijing Inst Radiat Med, Beijing Proteome Res Ctr, State Key Lab Prote, Beijing 102206, Peoples R China

[5] Natl Univ Def Technol, Coll Mechatron & Automat, Dept Automat Control, Changsha 410073, Hunan, Peoples R China

[6] Acad Mil Med Sci, Affiliated Hosp, Dept Stomatol, Beijing 100071, Peoples R China

来源：

JOURNAL OF PROTEOME RESEARCH | 2013年 / 12卷 / 01期

基金：

中国国家自然科学基金;

关键词：

proteomic data; chromosome-centric visualization; proteome browser; human genome annotation; bioinformatics; Chromosome-Centric Human Proteome Project; MASS-SPECTROMETRY; GENOME BROWSER; IDENTIFICATION; RESOURCE; SYSTEM;

D O I：

10.1021/pr300831z

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

High-throughput mass spectrometry and antibody-based experiments have begun to produce a large amount of proteomic data sets. Chromosome-based visualization of these data sets and their annotations can help effectively integrate, organize, and analyze them. Therefore, we developed a web-based, user-friendly Chromosome-Assembled human Proteome browsER (CAPER). To display proteomic data sets and related annotations comprehensively, CAPER employs two distinct visualization strategies: track-view for the sequence/site information and the correspondence between proteome, transcriptome, genome, and chromosome and heatmap-view for the qualitative and quantitative functional annotations. CAPER supports data browsing at multiple scales through Google Map-like smooth navigation, zooming, and positioning with chromosomes as the reference coordinate. Both track-view and heatmap-view can mutually switch, providing a high-quality user interface. Taken together, CAPER will greatly facilitate the complete annotation and functional interpretation of the human genome by proteomic approaches, thereby making a significant contribution to the Chromosome-Centric Human Proteome Project and even the human physiology/pathology research. CAPER can be accessed at http://www.bprc.ac.cn/CAPE.

引用

页码：179 / 186

页数：8

共 24 条

[21] The Proteomics Identifications database: 2010 update [J].

Vizcaino, Juan Antonio ;

Cote, Richard ;

Reisinger, Florian ;

Barsnes, Harald ;

Foster, Joseph M. ;

Rameseder, Jonathan ;

Hermjakob, Henning ;

Martens, Lennart .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D736-D742

[22] Toward an understanding of the protein interaction network of the human liver [J].

Wang, Jian ;

Huo, Keke ;

Ma, Lixin ;

Tang, Liujun ;

Li, Dong ;

Huang, Xiaobi ;

Yuan, Yanzhi ;

Li, Chunhua ;

Wang, Wei ;

Guan, Wei ;

Chen, Hui ;

Jin, Chaozhi ;

Wei, Junchen ;

Zhang, Wanqiao ;

Yang, Yongsheng ;

Liu, Qiongming ;

Zhou, Ying ;

Zhang, Cuili ;

Wu, Zhihao ;

Xu, Wangxiang ;

Zhang, Ying ;

Liu, Tao ;

Yu, Donghui ;

Zhang, Yaping ;

Chen, Liang ;

Zhu, Dewu ;

Zhong, Xing ;

Kang, Lixin ;

Gan, Xiang ;

Yu, Xiaolan ;

Ma, Qi ;

Yan, Jing ;

Zhou, Li ;

Liu, Zhongyang ;

Zhu, Yunping ;

Zhou, Tao ;

He, Fuchu ;

Yang, Xiaoming .

MOLECULAR SYSTEMS BIOLOGY, 2011, 7

[23] A dataset of human fetal liver proteome identified by subcellular fractionation and multiple protein separation and identification technology [J].

Ying, Wantao ;

Jiang, Ying ;

Guo, Lihai ;

Hao, Yunwei ;

Zhang, Yangjun ;

Wu, Songfeng ;

Zhong, Fan ;

Wang, Jinglan ;

Shi, Rong ;

Li, Dong ;

Wan, Ping ;

Li, Xiaohai ;

Wei, Handong ;

Li, Jianqi ;

Wang, Zhongsheng ;

Xue, Xiaofang ;

Cai, Yun ;

Zhu, Yunping ;

Qian, Xiaohong ;

He, Fuchu .

MOLECULAR & CELLULAR PROTEOMICS, 2006, 5 (09) :1703-1707

[24] Regulation of Cellular Metabolism by Protein Lysine Acetylation [J].

Zhao, Shimin ;

Xu, Wei ;

Jiang, Wenqing ;

Yu, Wei ;

Lin, Yan ;

Zhang, Tengfei ;

Yao, Jun ;

Zhou, Li ;

Zeng, Yaxue ;

Li, Hong ;

Li, Yixue ;

Shi, Jiong ;

An, Wenlin ;

Hancock, Susan M. ;

He, Fuchu ;

Qin, Lunxiu ;

Chin, Jason ;

Yang, Pengyuan ;

Chen, Xian ;

Lei, Qunying ;

Xiong, Yue ;

Guan, Kun-Liang .

SCIENCE, 2010, 327 (5968) :1000-1004

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