TY - JOUR
T1 - CanProVar 2.0
T2 - An Updated Database of Human Cancer Proteome Variation
AU - Zhang, Menghuan
AU - Wang, Bo
AU - Xu, Jia
AU - Wang, Xiaojing
AU - Xie, Lu
AU - Zhang, Bing
AU - Li, Yixue
AU - Li, Jing
N1 - Funding Information:
^^This work was supported by the National Natural Science Foundation of China (31271416), the National Key Basic Research Program (2011CB910204, 012CB910102), the Chinese Human Proteome Projects (CNHPP: 2014DFB30030 and 2014DFB30020), and National Key Research and Development Plan (2016YFC0902403). B.Z. was supported by National Cancer Institute (NCI) CPTAC Award No. U24CA210954.
Publisher Copyright:
© 2016 American Chemical Society.
PY - 2017/2/3
Y1 - 2017/2/3
N2 - Identification and annotation of the mutations involved in oncogenesis and tumor progression are crucial for both cancer biology and clinical applications. Previously, we developed a public resource CanProVar, a human cancer proteome variation database for storing and querying single amino acid alterations in the human cancers. Since the publication of CanProVar, extensive cancer genomics efforts have revealed the enormous genomic complexity of various types of human cancers. Thus, there is an overwhelming need for comprehensive annotation of the genomic alterations at the protein level and making such knowledge easily accessible. Here, we describe CanProVar 2.0, a significantly expanded version of CanProVar, in which the amount of cancer-related variations and noncancer specific variations was increased by about 10-fold as compared to the previous version. To facilitate the interpretation of the variations, we added to the database functional data on potential impact of the cancer-related variations on 3D protein interaction and on the differential expression of the variant-bearing proteins between cancer and normal samples. The web interface allows for flexible queries based on gene or protein IDs, cancer types, chromosome locations, or pathways. An integrated protein sequence database containing variations that can be directly used for proteomics database searching can be downloaded.
AB - Identification and annotation of the mutations involved in oncogenesis and tumor progression are crucial for both cancer biology and clinical applications. Previously, we developed a public resource CanProVar, a human cancer proteome variation database for storing and querying single amino acid alterations in the human cancers. Since the publication of CanProVar, extensive cancer genomics efforts have revealed the enormous genomic complexity of various types of human cancers. Thus, there is an overwhelming need for comprehensive annotation of the genomic alterations at the protein level and making such knowledge easily accessible. Here, we describe CanProVar 2.0, a significantly expanded version of CanProVar, in which the amount of cancer-related variations and noncancer specific variations was increased by about 10-fold as compared to the previous version. To facilitate the interpretation of the variations, we added to the database functional data on potential impact of the cancer-related variations on 3D protein interaction and on the differential expression of the variant-bearing proteins between cancer and normal samples. The web interface allows for flexible queries based on gene or protein IDs, cancer types, chromosome locations, or pathways. An integrated protein sequence database containing variations that can be directly used for proteomics database searching can be downloaded.
KW - cancer
KW - database
KW - proteome
KW - variation
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U2 - 10.1021/acs.jproteome.6b00505
DO - 10.1021/acs.jproteome.6b00505
M3 - Article
C2 - 27977206
AN - SCOPUS:85011655831
SN - 1535-3893
VL - 16
SP - 421
EP - 432
JO - Journal of Proteome Research
JF - Journal of Proteome Research
IS - 2
ER -