Download CanProVar Data

CanProVar provides the download of human protein database (Ensembl v79) in the fasta format, in which variation information is recorded in the header line of each sequence. The README file explains the contents of the following files:

Total

	Description	Protein(FASTA)	Statistics
Validated dbSNP_nsSNPs	variation information from validated coding SNPs	dbSNP_validated_nsSNP_protein	967,017
Cancer related_nsSNPs	mutations that have been reported in cancer samples	cancer_nsSNP_protein	156,671
Both	nsSNPs from both the dbSNP_validated* file and the cancer_* file	all_nsSNP_protein	1123,688

The csSNPs of each cancer type

Cancer Name	Statistics	Protein(FASTA)
Adrenal Gland Neoplasms	15
Biliary Tract Cancer	570
Bone Neoplasms	415
Brain Cancer	327
Breast Cancer	17460
Central Nervous System Neoplasms	5905
Colorectal Cancer	1127
Esophageal Cancer	2246
Gastric Cancer	6693
Head and Neck Cancer	9450
Hepatocellular Carcinoma	5143
Intestines Cancer	18090
Leukemia	8134
Lung Cancer	14382
Lymphoma	1110
Melanoma	11659
Myeloproliferative Disorders	53
Neoplasms by Histologic Type	1491
Non-small cell lung carcinoma	60
Oral Cancer	3
Ovarian Cancer	17303
Pancreatic Cancer	6353
Parathyroid Carcinoma	240
Pituitary Carcinoma	140
Prostate Cancer	1804
Renal Cancer	4183
Sarcoma	31
Skin Cancer	6137
Small cell lung carcinoma	34
Testicular Cancer	91
Thyroid Carcinoma	1804
Urinary Bladder Cancer	3718
Uterine Cancer	8594
Vulva Cancer	172
acute lymphocytic leukemia	6
acute myeloid leukemia	8
breast ductal carcinoma	23
chronic lymphocytic leukemia	198
chronic myeloid leukemia	21
follicular thyroid carcinoma	4
pancreatic ductal adenocarcinoma	11

Download MS-CanProVar Data

	Protein Sequence Database
MS-CanProVar (version 2.0)	MS-CanProVar2

MS-CanProVar (version 2.0) is a protein sequence database that includes variation information to facilitate peptide variant detection in shotgun proteomics. In the .fasta file, each variant peptide is included as an independent entry; variations are annotated in the header line; variations are labeled as "rs" for SNPs and "cs" for cancer-related mutations. Please refer to A bioinformatics workflow for variant peptide detection in shotgun proteomics. Li et al., MCP, 2011 for details about the MS-CanProVar database. The current version of MS-CanProVar is based on Ensembl V79.