Results - pathways, GO terms and compounds

How are the pathways/GO terms/compounds results scored and ranked?

This binomial distribution is used to test the null hypothesis that the user’s input genes are not over-represented within any SuperPath, GO term or compound in the databases from which GeneAnalytics extracts its data (See Resources and statistics).

The presented score is a transformation (-log2) of the resulting p-value, where higher scores indicate better matches.

The score range is divided into three levels of quality, based on the p-value corrected for the multiple comparisons (using the false discovery rate method):

High: corrected p-value smaller or equal to 0.0001.

Medium: corrected p-value higher than 0.0001 but smaller or equal to 0.05.

Low: corrected p-value higher than 0.05.

The score is presented by a score bar whose color indicates the match quality: dark green for high, light green for medium and beige for low.  This graphic visualization of the score enables the user to evaluate the overall quality of the results.

Results are ranked in descending order of their score. If several matches have the same score, they are ordered by the ratio of matched to total number of genes in the entity (from highest to lowest).

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