Chromosome 7-centric analysis of proteomics data from a panel of human colon carcinoma cell lines

J Proteome Res. 2013 Jan 4;12(1):89-96. doi: 10.1021/pr300906y. Epub 2012 Dec 18.


In this manuscript, we describe a shotgun proteomics approach for a comprehensive proteomic analysis of samples including total lysates, membrane, secretome, and exosome fractions from a panel of colorectal cancer cell lines. We will present an analysis of our proteomics data in two alternative formats. First we will discuss a traditional analysis of our data, in which we identify a number of cancer-associated proteins using various proteomic data analysis tools. In a second approach, we use a chromosome format to organize the proteomic data on chromosome 7, allowing the identification of clusters of cancer-associated genes with boundaries defined by physical proximity on different chromosomes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Carcinoma / genetics
  • Carcinoma / metabolism
  • Cell Line, Tumor
  • Chromosome Deletion
  • Chromosomes, Human, Pair 7* / genetics
  • Chromosomes, Human, Pair 7* / metabolism
  • Colonic Neoplasms* / genetics
  • Colonic Neoplasms* / metabolism
  • Databases, Protein
  • Genome, Human
  • Human Genome Project
  • Humans
  • Proteins* / classification
  • Proteins* / genetics
  • Proteins* / metabolism
  • Proteome*


  • Proteins
  • Proteome