Among the suppressed genes more than 20%% of them were annotated to the regulation of cell proliferation, blood vessel development, DNA metabolic process, regulation of programmed cell death and regulation of cell cycle.
The first gene, mam3, is annotated to encode the M cell agglutinin [ 20], and hence, its expression was expected to be M-cell specific.
Among the PCCGs, we calculated the proportion of genes which are annotated to participate in the cell cycle process (in MIPS database) and used the hyper-geometric distribution to define the p-values.
For example, one would expect the genes in class 111 to be annotated to core processes of the cell cycle.
Thirty-seven genes were grouped with a role in cell-cycle progression, whereas 25 genes were annotated to participate in some aspects of cell division (Additional file 14: Table S13).
The prominent open reading frames identified are annotated to have regulatory, transcriptional, translation, or cell envelope biogenesis functions, or are classified as only having hypothetical functions.
As the most over-represented GO term, "cell cycle" was annotated to 36.5% of genes (19/52).
Seven of these are annotated to the G1/S phase of the cell cycle, six of which have reported E2F1 responses that are concordant with NO effects in the current experiment.
This pair has a hit similarity of 0.54 (it shares 25 hits of the 51 and 25 tested compounds in each assay, respectively) and a biological similarity of 1 (the same 'GO 0016049 cell growth' term was annotated to both assays).
Many of the cluster III genes are also annotated to cell cycle progression and response to nutrients and had similar regulation in all strains.
