Simple enrichment analysis

RENATO's simple enrichment analysis is based on the implementation of the FatiGO method published by Al-Shahrour et al. (2004). This FatiGO implementation takes a list of genes (see Input file formats) and try to identify common regulatory elements to this target's list.

For every gene in the input list REANTO extract its annotated regulators in the selected database. Then a Fisher's exact test using a 2×2 contingency tables is used to check for significant over-representation of each regulatory element in the gene list with respect to the regulation in the genome. In the following figure we try to summarize this process. Our gene list contains targets for GATA1 (orange balls) and SP1 (blue balls) transcription factors (TFs). For each TF, we extract the proportion of targets in the gene list and in the genome to construct the contingency table. Fisher's exact test is used to determine if there is a nonrandom association between the gene list and the specific regulation of a TF.

The process is analog for miRNAs.

Multiple testing correction

When a test is repeated multiple times, like RENATO, that applies a test for each regulator, the expected proportion of false significant results increase. To solve this problem, a multiple testing correction method must be applied to estimate or control the proportion of test incorrectly called significant. To prevent this from happening, RENATO corrects the obtained Fisher's p-value with the False discovery rate (FDR) method.

simple_enrichment_analysis.txt · Last modified: 2012/04/20 18:50 by mbleda
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