Prioritization:Pathways
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== Proximity measure == | == Proximity measure == | ||
| - | The proximity measure implemented is currently the following. It consists of computing the over-represented pathways in the provided set if know genes and then use the Fisher omnibus procedure to combine the p-values of the pathways in which a candidate gene is involved. See [http://www.nature.com/nbt/journal/v24/n5/abs/nbt1203.html Aerts ''et al.'', 2006 | + | The proximity measure implemented is currently the following. It consists of computing the over-represented pathways in the provided set if know genes and then use the Fisher omnibus procedure to combine the p-values of the pathways in which a candidate gene is involved. See [http://www.nature.com/nbt/journal/v24/n5/abs/nbt1203.html Aerts ''et al.'', 2006] for more information. |
== Data == | == Data == | ||
There is currently only one dataset available for ''Escherichia coli''. The BioCyc/EcoCyc pathway data version 13.6 were downloaded and used. For each pathway, the set of genes involved is extracted and used as described in the ''Proximity measure section''. | There is currently only one dataset available for ''Escherichia coli''. The BioCyc/EcoCyc pathway data version 13.6 were downloaded and used. For each pathway, the set of genes involved is extracted and used as described in the ''Proximity measure section''. | ||
Revision as of 13:28, 21 January 2011
Proximity measure
The proximity measure implemented is currently the following. It consists of computing the over-represented pathways in the provided set if know 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
There is currently only one dataset available for Escherichia coli. The BioCyc/EcoCyc pathway data version 13.6 were downloaded and used. For each pathway, the set of genes involved is extracted and used as described in the Proximity measure section.
