Extracted GO terms were used in FatiGO within the Babelomics suite [ 66] for functional over-representation analysis.
For BiNGO, we use the combined and filtered gene set as the reference set, the hypergeometric test as the test for functional over-representation, and False Discovery Rate (FDR) as the multiple hypothesis testing correction scheme.
The tool DAVID [ 24] was used for the calculation of the functional over-representation statistics of the different lists of significant genes obtained with Rank Prod analysis.
Another previous search for functional RNAs over the human genome using EvoFold [8] found many more high-scoring motifs in 3' UTR regions than in 5' UTR regions.
The cortical response to these stimuli requires the encoding of identical values for functional parameters over the surface of visual cortex.
Ranked results from Top Networks, Bio-Functions, Tox-Functions, and Canonical Pathways meeting minimal p value <0.05 for each pathway containing at least three focus molecules were queried for functional annotations and over-represented pathways to facilitate the biological interpretation of selected gene lists.
The functional clustering tool was used to look for functional enrichment for genes over- and under-expressed more than two-fold in Alzheimer's disease.
Then, DAVID tool was used to look for functional enrichment for genes over- and under-expressed more than two-fold in our samples.
The functional clustering tool was used to look for functional enrichment for genes over- and under-expressed more than two-fold between the pools.
Evidence for functional consequences of TRAIL over-expression in autoimmune diseases including rheumatoid arthritis has emerged from gene therapy studies [ 32].
This Hyers-Ulam stability is a classical type of stability, but there is another kind of stability introduced by Risteski [9] for functional equations spanned over an -dimensional complex vector space too.
