The differentially expressed genes were analyzed using the GOstat program (available at www.gostat.wehi.edu.au), which identifies enriched functional groups of genes based on Gene-Ontology (GO) annotations.
A statistical analysis using the GOstat program [ 18] confirmed the enrichment of Chinese chestnut transcritpome in these functional categories (p-value < 0.01).
Gene Ontology term enrichment in up and down regulated gene sets were assessed using the GOstat web tool [37].
p-values were calculated by hypergeometric test using the GOstat module from Bioconductor.
In the first one, GO enrichment analysis was performed using the GOStat tool [ 24].
Over- and under-represented ontologies, with respect to the Drosophila genome, were Drosophila melanogaster homologies using the GOstat tool [ 38].
Functional annotation of differentially expressed genes was performed using the DAVID web-server [ 69] and GOstat [ 70]..For GOStat analysis, all significantly down-regulated transcripts with at least one associated GO description (39), previously obtained with Blast2GO, were compared against a background of 4,692 GO-annotated DLPD entries, using the GOStat program with default settings.
To gain an overview of the predominant molecular functions and biologic pathways that were regulated at the transcriptional level during the uterotrophic response to E2, we interrogated the 3,538 E2-responsive genes using the GOStat gene ontology mining tool (http://gostat.wehi.edu.au) (Beissbarth and Speed 2004).
We analyzed the functional enrichment of genes contained in the CNVRs from the Korean population using the GOstat tool (Table 4 and 5) [ 29].
Using the GOStat program for gene ontology analysis (, [ 31]), the most overrepresented GO category for the green module was in response to temperature stimulus (GO 0009408, p = 4.4 × 10-22).
To determine whether categories of genes with particular biological function were associated with different seed phenotypes, we looked for GO (gene ontology) biological process terms [ 40] that were over- or underrepresented among genes showing differential expression, using the GOstat tool available at http://gostat.wehi.edu.au[ 41].
