Download CanProVar Data

CanProVar provides the download of human protein database (Ensembl v69) 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	822,259
Cancer related_nsSNPs	mutations that have been reported in cancer samples	cancer_nsSNP_protein	65,199
Both	nsSNPs from both the dbSNP_validated* file and the cancer_* file	all_nsSNP_protein	885,747

The csSNPs of each cancer type

Cancer Name	Statistics	Protein(FASTA)
Adrenal Gland Neoplasms	16
Biliary Tract Cancer	55
Brain Cancer	257
Breast Cancer	13036
breast ductal carcinoma	23
Central Nervous System Neoplasms	2432
Colorectal Cancer	1142
Esophageal Cancer	37
Gastric Cancer	665
Head and Neck Cancer	7381
Hepatocellular Carcinoma	2050
Intestines Cancer	1518
Leukemia	49
acute lymphocytic leukemia	6
acute myeloid leukemia	8
chronic lymphocytic leukemia	201
chronic myeloid leukemia	21
Liver Cancer	26
Lung Cancer	2937
Lymphoma	1178
Melanoma	4314
Myeloproliferative Disorders	59
Neoplasms by Histologic Type	1666
Non-small cell lung carcinoma	61
Oral Cancer	3
Ovarian Cancer	18703
Pancreatic Cancer	4554
pancreatic ductal adenocarcinoma	11
Pituitary Carcinoma	13
Prostate Cancer	145
Renal Cancer	820
Sarcoma	31
Skin Cancer	5437
Small cell lung carcinoma	35
Testicular Cancer	20
Thyroid Carcinoma	182
follicular thyroid carcinoma	4
Urinary Bladder Cancer	32
Uterine Cancer	271

Download MS-CanProVar Data

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 V68.