Technical Overview,

From TheGPMWiki
Jump to: navigation, search

This script lists the KEGG pathways for the proteins found in a GPMDB file.

The required arguments are path, proex and ltype. path is the file system path to the GPM result file. proex is used to create links to other scripts on GPMDB. ltype controls the appearance of display elements on the page. Optional parameters are npep, taxa, k, all, down, up and same, all of which are used in generating links to additional GPM resources.

Display Elements

  • a list of links to other resources on the GPM.
  • a form to control the display of proteins from the GPM result file, depending on their expected vs observed distribution within the GPM result file being viewed.
  • The result table:
    • KEGG ID: the identifier for the specific pathway.
    • Pathway: the name of the pathway.
    • log(I): the base-10 logarithm of the raw intensities observed for the proteins within a single pathway.
    • log(p)+: the base-10 logarithm of the chances that the collection of proteins assigned to this pathway is random.
    • protein description: a compound field:
      • a bar graph depicting whether or not the proteins in this pathway are over-represented (enriched), expected or under-represented (depleted) if the protein identifications are uniformly distributed.
      • X/Y of Z: X is the number of proteins from the GPM file that fall in this pathway; Y is the number that would be expected if the proteins were uniformly distributed, and Z is the number of proteins assigned to this KEGG pathway.
      • a text description of the proteins belonging to this KEGG pathway.
Personal tools