Mutated Genes, Pathways, Processes and protein Domains in tumours web application.

Tutorial

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Combining many sources of information, we were able to create a dataset containing more than 5,000 genes mutated in cancers. A Fisher's test has been applied to identify pathways (Kegg, Biocarta and Reactome), processes (Gene Ontology Biological Process) and protein domains (Interpro) that contain more mutated genes than expected by chance. The webtool is dedicated to search and parse the results of this study.

How to browse the results

  • Select one or more tumour type
  • Select one or more pathway/process/domain database.
    • Overall, to focus on cellular pathways, select Kegg, Reactome and Biocarta. To focus on biological processes, select Gene Ontology, and to focus on protein domains, select Interpro
  • Select if you want to display results common to several tumour types or specific to a tumour type or both
  • Select a statistical theshold. Three threshold Q-values, Q-value<0.001 (very significant), Q-value<0.01 (significant) and Q-value<0.1 (medium) are available, and describe the probability of obtaining such a number of mutated genes in the corresponding pathway/process/domain family, by chance alone.
  • The pathways/process/domains statistically enriched (according to the selected threshold) in the selected tumour types are represented as a graph.
  • The edges in the graph are white when the pathways/process/domains is statistically enriched in more than one tumour type (common), and yellow when it is significant only in one tumours type (specific) (according to the selected threshold).

How to search by keywords

Pathways, processes and protein domains can be searched by keywords. Gene names can be searched by HUGO standard gene names or Ensembl Ids.