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Figure 2 | BMC Bioinformatics

Figure 2

From: Seeking unique and common biological themes in multiple gene lists or datasets: pathway pattern extraction pipeline for pathway-level comparative analysis

Figure 2

The interface of the PPEP for batch computation of Fisher's exact test of multiple gene lists and merging the result files for matrix of enrichment scores. From each species-specific database, multiple functional categories can be selected for batch computation. Users have options merging p-values for enrichment scores, merging ListHits (how many genes from the lists hit the term), or merging -log10 transformed FDR values into a matrix. As default, Fisher's exact test p-values can be floored by criteria of p > 0.05 and ListHits <= 1 to make the corresponding enrichment scores as 0. However, users have options to either not floor the enrichment scores, or set up their own customized way to do the flooring. Other options are also provided: e.g., computing FDRs or not, or number of iterations for FDR computations.

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BMC Bioinformatics

ISSN: 1471-2105

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