Data mining tools for the SUM breast cancer cell lines

  • SUM line Gene query tool:
    • This search engine allows users of the SLKBase to obtain the functional, genomic, expression, and druggability status of any gene for all cell lines in the data base.  The list that is generated by this search engine rank orders cell lines by the essentialness of the searched gene for all of the cell lines
  • Oncogene signature tool:
    • This tool allows users of the SLKBase to view a list of functional oncogenes, candidate oncogenes, and potential oncogenes for any cell line in the data base with one mouse click
  • KEGG Pathway Engine:
    • This tool allows users of the SLKBase to view the shRNA screen data or the gene expression data as as they map to any KEGG pathway
  • KEGG Pathway Analysis:
    • This tool allows users to determine, in rank order, the most essential pathway in each breast cancer cell line.  The “essentialness” for each cell line is determined using an algorithm that considers the fractional enrichment of a pathway with genes that were hits in the shRNA screen, and the hit genes are weighted if they are directly connected in the pathway with other hit genes, and weighted further of they are genomically altered.
  • KEGG Pathway Druggable Functional Pathway Analysis:
    • This tool is similar to the KEGG Pathway Analysis tool but this tool only considers those KEGG pathways that have hits in the screen that are druggable, and the Pathways are rank ordered by their essentialness AND by their druggability
  • Proteomic and phospho-proteomic search tool:
    • This tool allows users of the SLKBase to obtain the normalized linear expression values for any of the proteins or phospho-proteins that were queried using the Reverse Phase protein array.