Algorithm to test for enrichment |

The test for enrichment is done using the Fisher's exact test with a multiple-testing extension. We use the false discovery rate. For each of the p-value-thresholds alpha, we determine the number of false discoveries (NFD), and the number of total discoveries (NP), i.g. how many factors we see with p-value < alpha. The false discovery rate is then simply given by formula 1: Now, the NFD can be determined using the hypergeometric distribution, simply by summing all configurations for the Fisher's test: with the hypergeometric distribution beeing defined by: If you are further interested in this method, we recommend the following articles: Blüthgen, N., Kielbasa, S. M and Herzel, H. Inferring combinatorial regulation of transcription in silico. Blüthgen, N., Brand, K., Cajavec, B., Swat, M., Herzel, H. and Beule, D. Biological profiling of gene groups utilizing Gene Ontology. |