Prioritization:Pathways

From silico.biotoul.fr

Proximity measure

The proximity measure implemented is currently the following. It consists of computing the over-represented pathways in the provided set if known genes and then use the Fisher omnibus procedure to combine the p-values of the pathways in which a candidate gene is involved. See Aerts et al., 2006 for more information.

Data

The BioCyc pathways data were downloaded and used. For each pathway, the set of genes involved is extracted and used as described in the Proximity measure section.

Datasets:

• Bacillus subtilis 168 (BioCyc version 13.6)
• Escherichia coli K12 (v13.6)
• Halobacterium sp. NRC-1 (v13.6)
• Pseudomonas aeruginosa PAO1 (v13.6)
• Staphylococcus aureus NCTC 8325 (v13.6)
• Shigella flexneri 301 (v14.5)