An Unsupervised Approach to Predict Functional Relations between Genes Based on Expression Data

Table 2

Richness of similar function genes in selected clusters. For each cluster, hypergeometric 𝑃-values, corresponding GO terms, and also the actual number of genes of a particular function are indicated.

CID	Total number of genes	𝑃-value/GO ID; (From GOstats result)	Some relevant GO terms (corresponding number of genes); (From SGD database)
4	97	1.20𝐸−131/GO:0022626 (CC); 2.62𝐸−117/GO:0002181 (BP); 4.80𝐸−129/GO:0003735 (MF)	Cytosolic ribosome (94), structural constituent of ribosome (94), cytoplasmic translation (93), ribosome (96)
16	76	6.42𝐸−24/GO:0044391 (CC); 7.23𝐸−17/GO:0006412 (BP)	Ribosomal subunit (37), structural molecule activity (38)
19	73	3.29𝐸−23/GO:0030529 (CC)	Ribonucleoprotein complex (47), intracellular part (73)
226	8	1.50𝐸−20/GO:0000788 (CC); 1.93𝐸−14/GO:0006333 (BP)	Nuclear nucleosome (8), DNA bending complex (8)
1	113	1.42𝐸−17/GO:0042254 (BP)	Cellular metabolic process (104), intracellular part (109)
44	34	2.89𝐸−16/GO:0005840 (CC)	Cytosolic part (21), cytoplasm (34)
35	44	3.35𝐸−16/GO:0010467 (BP)	Gene expression (41), primary metabolic process (43)
85	17	4.76𝐸−14/GO:0044429 (CC)	Mitochondrial part (14), mitochondrion (16)
155	11	6.28𝐸−14/GO:0051082 (MF); 4.97𝐸−13/GO:0006457 (BP)	Protein folding (9), protein binding (11), cellular protein metabolic process (10)
278	7	3.00𝐸−13/GO:0000502 (CC)	Proteasome complex (7), proteasome storage granule (5)
87	16	5.26𝐸−13/GO:0005730 (CC)	Nucleolus (12), non-membrane-bounded organelle (14)
107	14	1.97𝐸−12/GO:0007005 (BP)	Mitochondrion organization (12), cellular component organization (13)
121	13	5.32𝐸−12/GO:0006094 (BP)	Glycolysis (7), generation of precursor metabolites and energy (9)
442	5	1.55𝐸−11/GO:0022904 (BP)	Mitochondrial respiratory chain (5), oxidoreductase complex (5)
173	10	1.56𝐸−11/GO:0006457 (BP); 2.58𝐸−08/GO:0051082 (MF)	Protein folding (7), unfolded protein binding (5), protein binding (8)
282	7	5.58𝐸−11/GO:0004298 (MF)	Modification-dependent protein catabolic process (7), roteasomal ubiquitin-independent protein catabolic process (5)
71	15	5.90𝐸−11/GO:0005840 (CC)	Ribosome (13), ribonucleoprotein complex (14)
725	3	1.61𝐸−09/GO:0003993 (MF)	Acid phosphatase activity (2)
214	9	2.88𝐸−09/GO:0008121 (MF)	Hydrogen ion transmembrane transporter activity (5), single-organism metabolic process (7)
736	3	4.03𝐸−09/GO:0004067 (MF)	Asparaginase activity (3)
1092	3	2.26𝐸−08/GO:0015002 (MF)	Heme-copper terminal oxidase activity (3)
270	7	2.32𝐸−08/GO:0015078 (MF)	Ion transmembrane transporter activity (6)