Table 4.
Over-represented GO terms for one of the fused clusters extracted from the galactose utilization dataset (with w=0.5
| GO ID | Cluster | P-value | Count (fused) | Count (Liu) | GO term |
|---|---|---|---|---|---|
| 4365 | 1 | 9.8 × 10−6 | 2/4 | 3/9 | Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) activity |
| 16 620 | 1 | 5.0 × 10−4 | 2/4 | 3/9 | Oxidoreductase activity, acting on aldehyde/oxo donors, NAD/NADP acceptor |
| 51 287 | 1 | 1.1 × 10−3 | 2/4 | 3/9 | NAD or NADH binding |
| 6096 | 1 | 3.6 × 10−8 | 4/4 | 9/9 | Glycolysis |
| 19 320 | 1 | 3.3 × 10−7 | 4/4 | 9/9 | Hexose catabolic process |
| 46 164 | 1 | 7.4 × 10−7 | 4/4 | 9/9 | Alcohol catabolic process |
| 16 052 | 1 | 3.3 × 10−6 | 4/4 | 9/9 | Carbohydrate catabolic process |
| 6094 | 1 | 1.9 × 10−5 | 3/4 | 7/9 | Gluconeogenesis |
| 46 364 | 1 | 1.2 × 10−4 | 3/4 | 7/9 | Monosaccharide biosynthetic process |
| 19 752 | 1 | 5.7 × 10−4 | 4/4 | 8/9 | Carboxylic acid metabolic process |
| 42 180 | 1 | 6.4 × 10−4 | 4/4 | 8/9 | Cellular ketone metabolic process |
| 6082 | 1 | 6.8 × 10−4 | 4/4 | 8/9 | Organic acid metabolic process |
| 6800 | 1 | 1.2 × 10−3 | 2/4 | 3/9 | Oxygen and reactive oxygen species metabolic process |
| 1950 | 1 | 1.7 × 10−4 | 3/4 | 7/9 | Plasma membrane enriched fraction |
| 5626 | 1 | 2.1 × 10−3 | 3/4 | 7/9 | Insoluble fraction |
| 5811 | 1 | 3.3 × 10−3 | 2/4 | 3/9 | Lipid particle |
| 16 251 | 2 | 8.9 × 10−5 | 5/23 | 7/84 | General RNA polymerase II transcription factor activity |
| 30 528 | 2 | 1.6 × 10−3 | 6/23 | 26/84 | Transcription regulator activity |
| 31 202 | 2 | 1.6 × 10−3 | 4/23 | 22/84 | RNA splicing factor activity, transesterification mechanism |
| 3677 | 2 | 6.1 × 10−3 | 6/23 | 14/84 | DNA binding |
| 16 070 | 2 | 9.2 × 10−12 | 19/23 | 53/84 | RNA metabolic process |
| 10 467 | 2 | 1.1 × 10−7 | 22/23 | 78/84 | Gene expression |
| 398 | 2 | 1.5 × 10−4 | 6/23 | 24/84 | Nuclear mRNA splicing via spliceosome |
| 375 | 2 | 2.3 × 10−4 | 6/23 | 26/84 | RNA splicing, via transesterification reactions |
| 45 449 | 2 | 4.1 × 10−4 | 6/23 | 29/84 | Regulation of transcription |
| 80 090 | 2 | 7.5 × 10−4 | 13/23 | 40/84 | Regulation of primary metabolic process |
| 34 961 | 2 | 1.2 × 10−3 | 17/23 | 52/84 | Cellular biopolymer biosynthetic process |
| 9059 | 2 | 2.9 × 10−3 | 17/23 | 52/84 | Macromolecule biosynthetic process |
| 51 171 | 2 | 6.1 × 10−3 | 8/23 | 31/84 | Regulation of nitrogen compound metabolic process |
| 5634 | 2 | 2.6 × 10−8 | 22/23 | 15/84 | Nucleus |
| 32 991 | 2 | 7.9 × 10−5 | 18/23 | 24/84 | Macromolecular complex |
| 5681 | 2 | 1.3 × 10−4 | 5/23 | 19/84 | Spliceosomal complex |
| 43 227 | 2 | 3.9 × 10−4 | 23/23 | 83/84 | Membrane-bounded organelle |
| 3735 | 3 | 1.3 × 10−21 | 16/17 | 75/75 | Structural constituent of ribosome |
| 6412 | 3 | 3.4 × 10−10 | 13/17 | 49/75 | Translation |
| 43 284 | 3 | 4.4 × 10−8 | 17/17 | 75/75 | Biopolymer biosynthetic process |
| 34 645 | 3 | 1.2 × 10−7 | 17/17 | 75/75 | Cellular macromolecule biosynthetic process |
| 9058 | 3 | 4.2 × 10−6 | 17/17 | 49/75 | Biosynthetic process |
| 19 538 | 3 | 7.2 × 10−6 | 13/17 | 49/75 | Protein metabolic process |
| 34 960 | 3 | 4.8 × 10−4 | 17/17 | 75/75 | Cellular biopolymer metabolic process |
| 43 170 | 3 | 9.4 × 10−4 | 17/17 | 75/75 | Macromolecule metabolic process |
| 33 279 | 3 | 3.7 × 10−21 | 16/17 | 75/75 | Ribosomal subunit |
| 5829 | 3 | 1.1 × 10−13 | 16/17 | 74/75 | Cytosol |
| 22 627 | 3 | 3.2 × 10−11 | 8/17 | 33/75 | Cytosolic small ribosomal subunit |
| 43 232 | 3 | 8.3 × 10−10 | 16/17 | 75/75 | Intracellular non-membrane-bounded organelle |
| 22 625 | 3 | 1.1 × 10−9 | 8/17 | 41/75 | Cytosolic large ribosomal subunit |
| 32 991 | 3 | 1.5 × 10−6 | 16/17 | 75/75 | Macromolecular complex |
| 44 422 | 3 | 1.1 × 10−4 | 16/17 | 75/75 | Organelle part |
| 32 040 | 3 | 5.4 × 10−3 | 3/17 | 7/75 | Small-subunit processome |
| 51119 | 4 | 2.8 × 10−9 | 4/4 | 11/12 | Sugar transmembrane transporter activity |
| 5353 | 4 | 3.2 × 10−7 | 3/4 | 10/12 | Fructose transmembrane transporter activity |
| 15578 | 4 | 3.2 × 10−7 | 3/4 | 10/12 | Mannose transmembrane transporter activity |
| 5355 | 4 | 4.6 × 10−7 | 3/4 | 10/12 | Glucose transmembrane transporter activity |
| 22891 | 4 | 3.3 × 10−5 | 4/4 | 12/12 | Substrate-specific transmembrane transporter activity |
| 5215 | 4 | 1.2 × 10−4 | 4/4 | 12/12 | Transporter activity |
| 8645 | 4 | 1.2 × 10−9 | 4/4 | 9/12 | Hexose transport |
| 8643 | 4 | 9.7 × 10−9 | 4/4 | 11/12 | Carbohydrate transport |
| 55085 | 4 | 1.4 × 10−5 | 4/4 | 12/12 | Transmembrane transport |
| 51234 | 4 | 8.3 × 10−3 | 4/4 | 12/12 | Establishment of localization |
| 5886 | 4 | 5.0 × 10−3 | 3/4 | 11/12 | Plasma membrane |
Also shown is a comparison with the GO terms extracted by the Liu et al. method. There is a general trend that the fused clusters are more highly GO enriched. For example, we have highlighted in bold all the cases where a cluster from one method shows a percentage of GO enrichment (for a given term) that is at least 1.5 times higher than the other method. Note that only GO terms appearing only in both cases are shown.