Proteomics

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CPTAC, TCGA Cancer Proteome Study of Colorectal Tissue / Global Proteome Analysis of Normal Colon Epithelium Samples


ABSTRACT: Explore This Study at the NCI Proteomic Data Commons

The goal of the CPTAC, TCGA Cancer Proteome Study of Colorectal Tissue is to analyze the proteomes of TCGA tumor samples that have been comprehensively characterized by molecular methods (Cancer Genome Atlas Network, Nature 2012).

Ninety-five TCGA tumor samples were used in this study from 90 patients, with 5 samples representing different portions from the same tumor. The samples originated from two TCGA cohorts: 64 are from Colon Adenocarcinoma (COAD) samples and 31 are from the Rectum Adenocarcinoma (READ) collection. The primary data from the liquid chromatography-tandem mass spectrometry (LC-MS/MS) global proteomic profiling of each tumor sample is associated with a data set in the table below. This work was accomplished by the Proteome Characterization Center (PCC) at Vanderbilt University led by Dr. Daniel C. Liebler. Clinical data files contain both the human readable TCGA bar codes and the UUIDs for each sample.

Complete Data Analysis from Vanderbilt University as published in Nature (Zhang, B., et al., Nature (2014) doi:10.1038/nature13438 Published online) is available here.

Data available on this study page (peptide spectrum matches and protein reports) are from the CPTAC Common Data Analysis Pipeline.

COAD tumor sample genomic data can be downloaded from here.
READ tumor sample genomic data can be downloaded from here.

Colon tissue samples (ascending and descending) were obtained from 30 patients. Each sample was analyzed with label free global proteomic profiling. These colon samples, while derived from colon cancer subjects, did not contain tumor. Samples were obtained from the Jim Ayers Institute for Precancer Detection and Diagnosis. Data sets below are labeled with the patient identification number and contain data for both ascending and descending tissue samples. Data from colon tumor samples are available in the TCGA Colorectal Cancer study.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Dr. Daniel C. Liebler and Jim Ayers 

PROVIDER: MSV000079852 | MassIVE | Thu Jun 23 16:31:00 BST 2016

SECONDARY ACCESSION(S): PXD014834

REPOSITORIES: MassIVE

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Publications

Comprehensive molecular characterization of human colon and rectal cancer.

Nature 20120718 7407


To characterize somatic alterations in colorectal carcinoma, we conducted a genome-scale analysis of 276 samples, analysing exome sequence, DNA copy number, promoter methylation and messenger RNA and microRNA expression. A subset of these samples (97) underwent low-depth-of-coverage whole-genome sequencing. In total, 16% of colorectal carcinomas were found to be hypermutated: three-quarters of these had the expected high microsatellite instability, usually with hypermethylation and MLH1 silencin  ...[more]

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