This analysis shows that several biological processes were overrepresented among gene targets of these miRNAs: regulation of transcription, development and differentiation, ubiquitin cycle, signal transduction, transport, and tumor suppression (synonym category: regulation of progression through cell cycle) (FDR p<10−9).
Strikingly, we observed that the same biological processes were overrepresented in RNAi and physical interaction-inferred datasets (Table 2).
Other predictable categories of molecular function and biological processes were overrepresented: specific DNA binding (transcription factors), Wnt signaling, and cell migration, adhesion, and death.
Several GO biological processes were overrepresented among the 21 transcripts differentially expressed in both data sets, such as: stress response, alternative splicing, protein binding, and tissue development.
Enrichment analysis against GO was conducted using the DAVID interface for the resulting DE mRNA and protein lists to determine if any biological processes were overrepresented.
Gene Ontology (http://david.niaid.nih.gov/david/ease.htm) analysis of the 1,811 genes using EASE revealed that more than 30 biological processes were overrepresented in response to IR-induced DNA damage (Table 2).
These biological processes are overrepresented only in the leaf transcriptome analysis of Arabidopsis infested by DMB.
Then, we studied whether any specific GO biological process was overrepresented in all genes for that module, i.e., not only those that showed high breed variability.
This functional categorization was supported by probability values (Fig. 12) which yielded the measure of the likelihood that a particular biological process was overrepresented in a cluster compared with that expected by random selection from the SAM list.
IR processes were overrepresented, but the terms related to hematopoietic or lymphoid organ development (LY) and taxis (T) were also present on the list of enriched biological processes.
Some biological Panther processes are overrepresented in the lists of genes with a fold change >1.5 in both VAT and SAT (p < 0.05 after Bonferroni correction).
