The collected gene sets in MSigDB are based on gene annotations, known pathways, gene expression data, miRNA target genes and other factors [ 35].
As an insight into potential TFs that regulate the genes in this network, it is noteworthy that N-regulated bicluster 9 contains 17 transcription factors (based on AGRIS transcription factor annotation) whose regulation is by definition correlated with targets in N-bicluster 9, as well as with genes from other functional and unknown categories.
Interestingly, the sequences from Methylocystis strain SC2 and Methylocystis rosea SV97T appear to be merged with an extracytoplasmic function (ECF) sigma factor, at least based on the annotation [ 43].
Additional File 5 shows 1,508 UniGenes classified as transcription factors based on annotation by the COG database, accounting for 8.9% of the annotated UniGenes.
All methylated genes were annotated based on GO annotation.
There are a significantly large number of developmental genes among transcription factors, based on the GO annotation (215 out of 674, χ2 test p-value = 7.82 × 10-85), indicating a larger number of both trans-elements as well as cis-elements in the developmental gene network.
The indicator attribute assigner takes input from the risk factor recognition module and assigns appropriate indicator attribute based on dataset annotation guidelines [ 19].
A graphical representation of the predicted network is presented in Figure 3, where environmental factors with known physiological actions are colored coded based on MeSH annotation (see Additional File 2 for complete annotation of nodes).
In fact that paper provided p53 bound regions classified as enhancers based on ENCODE annotation or as proto-enhancers, where p53 could act as pioneer transcription factor.
A genome-scale metabolic model, iJM658, was reconstructed based on genome annotation and literature mining.
