COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines

Nucleic Acids Res. 2012 Jan;40(Database issue):D957-63. doi: 10.1093/nar/gkr959. Epub 2011 Nov 18.


Genome-wide pooled shRNA screens enable global identification of the genes essential for cancer cell survival and proliferation and provide a 'functional genetic' map of human cancer to complement genomic studies. Using a lentiviral shRNA library targeting approximately 16,000 human genes and a newly developed scoring approach, we identified essential gene profiles in more than 70 breast, pancreatic and ovarian cancer cell lines. We developed a web-accessible database system for capturing information from each step in our standardized screening pipeline and a gene-centric search tool for exploring shRNA activities within a given cell line or across multiple cell lines. The database consists of a laboratory information and management system for tracking each step of a pooled shRNA screen as well as a web interface for querying and visualization of shRNA and gene-level performance across multiple cancer cell lines. COLT-Cancer Version 1.0 is currently accessible at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line, Tumor
  • Databases, Genetic*
  • Genes, Essential*
  • Genes, Neoplasm*
  • Humans
  • Neoplasms / genetics*
  • Oligonucleotide Array Sequence Analysis
  • RNA Interference*
  • RNA, Small Interfering


  • RNA, Small Interfering