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For each term is reported the sub ontology to whom it belongs, the mean, minimum and maximum marginal posterior probability of being involved and the number of genes annotated in the list of LRGs and in total.
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The nodes of the GO network represent the GO terms annotated in the input gene list, and the edges denote the global similarities between any GO term pairs.
Gene Ontology (GO) terms that were statistically over-represented among genes annotated in these lists were assumed to be of potential functional significance.
Additional file 2: Complete list of validated miR targets annotated in the STAT3 signaling pathway (Biocarta) listed together with the correspondent miR.
Gene names and nucleotide positions are listed as annotated in the S. Typhimurium 14028s genome ([ 41 ]; NC_016856).
The minor allele frequency of minor SNPs in our constrained EST list corresponded to that annotated in the NCBI dbSNP.
For example, prior to GO enrichment analysis in this study, we determined the number of annotated genes in the list of deregulated transcripts and found that only 55% and 75% of the 14,327 genes on the Rat GeneChip 230 2.0 are annotated in the EBI and RGD association files, respectively (data not shown).
The numbers of genes that fell in major categories were normalized by the number of genes annotated in each list and were expressed in percentages.
Further genes involved in hormone metabolism and function are annotated on the lists in Additional file 5 table S5, S5.1-3.
Conserved octameric sequences in [ 14] were therefore re-annotated using the list in miRBase release 10.1.
The lipid A products are categorized based on those enzymes that were responsible for their modification and are annotated in Figure 5, as listed in the order of elution: PagL, unmodified BN2, LpxF + PagL, PagP, LpxF, LpxF, LpxF + PagL + PagP, and finally LpxF + PagP.
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