Table 6 Illustrative set of biologically significant BicNET’s modules: description of the highly enriched terms in the modules presented in Table 5 [74, 75]

DryGIN

G1

Histone modification; regulation of histone H3-K79 methylation, histone H2B ubiquitination, H2B conserved C-terminal lysine ubiquitination, H3-K4 methylation (4)

G2

Regulation of gluconeogenesis; glutamate metabolic and catabolic processes (2);nicotinamide riboside metabolic process; nicotinamide nucleotide biosynthetic process

G3

Positive and negative regulation of transcription from RNA polymerase II; Invasive growth response to glucose limitation and hyperosmotic salinity response by regulating RNA polymerase II (5)

G4

Meiotic anaphase I; activation of anaphase-promoting complex activity involved in meiotic cell cycle

G5

Negative reg. of phospholipid biosynthesis; lipid homeostasis; isopropylmalate and oxaloacetate transport

G6

Cotranslational protein targeting to membrane; protein insertion into mitochondrial membrane; protein import into peroxisome membrane; reg. sporulation; actin filament bundle assembly involved in cytokinesis

G7

Acetate fermentation, acetyl-CoA biosynthesis (from acetate), reg. transcription on exit from mitosis

STRING

S1

Response to hypoxia; oxidation-dependent protein catabolic process; anaerobic respiration; age-dependent response to reactive oxygen species; cellular response to oxidative stress

S2

Positive and negative reg. of mitotic and nuclear cell cycle, DNA replication, budding cell apical bud growth

S3

Transport of aerobic electron, acetyl-CoA, vacuolar transmembrane, amine, transport (5); ribose phosphate metabolic process; D-ribose metabolic and catabolic processes (2)

S4

Heterochromatin maintenance involved in chromatin silencing; sister chromatid segregation

S5

Cytoplasmic and mitochondrial translation (4); regulation of translational fidelity; ADP biosynthesis

S6

rRNA processing; separation, cleavage and maturation of SSU-rRNA (5); ribosomal (large subunit) biogenesis