Table 1.
The top 20 lists GO terms associated with Gene Cluster #7 by CLASSIFI and GO-Bayes
| GO ID | IA | nA | P-value | RankP | B-score | RankB | Group | GO name |
|---|---|---|---|---|---|---|---|---|
| GO:0019933 | 21 | 6 | 4.00E-04 | 1 | 0.7652 | 149 | a | cAMP-mediated signaling |
| GO:0005773 | 91 | 13 | 4.61E-04 | 2 | 0.7544 | 187 | b | Vacuole |
| GO:0001726 | 23 | 6 | 6.85E-04 | 3 | 0.7724 | 118 | b | Ruffle |
| GO:0007188 | 16 | 5 | 7.95E-04 | 4 | 0.8688 | 7 | a | G-protein signaling, coupled to cAMP nucleotide second messenger |
| GO:0007190 | 10 | 4 | 9.73E-04 | 5 | 0.6928 | 508 | a | Activation of adenylate cyclase activity |
| GO:0045762 | 10 | 4 | 9.73E-04 | 5 | 0.6582 | 778 | a | Positive regulation of adenylate cyclase activity |
| GO:0031281 | 10 | 4 | 9.73E-04 | 5 | 0.4976 | 3148 | a | Positive regulation of cyclase activity |
| GO:0051349 | 10 | 4 | 9.73E-04 | 5 | 0.4712 | 3545 | a | Positive regulation of lyase activity |
| GO:0019935 | 25 | 6 | 1.11E-03 | 9 | 0.7568 | 177 | a | Cyclic-nucleotide-mediated signaling |
| GO:0007189 | 5 | 3 | 1.12E-03 | 10 | 0.8346 | 27 | a | G-protein signaling, adenylate cyclase activating pathway |
| GO:0016757 | 57 | 9 | 1.71E-03 | 11 | 0.8716 | 6 | c | Transferase activity, transferring glycosyl groups |
| GO:0000323 | 80 | 11 | 1.74E-03 | 12 | 0.8276 | 33 | b | Lytic vacuole |
| GO:0005764 | 80 | 11 | 1.74E-03 | 12 | 0.8762 | 5 | b | Lysosome |
| GO:0010324 | 69 | 10 | 1.87E-03 | 14 | 0.5084 | 2957 | b | Membrane invagination |
| GO:0006897 | 69 | 10 | 1.87E-03 | 14 | 0.5596 | 2015 | b | Endocytosis |
| GO:0007187 | 20 | 5 | 2.40E-03 | 16 | 0.8220 | 43 | a | G-protein signaling, coupled to cyclic nucleotide second messenger |
| GO:0006898 | 20 | 5 | 2.40E-03 | 16 | 0.5870 | 1601 | b | Receptor -mediated endocytosis |
| GO:0001609 | 2 | 2 | 2.45E-03 | 18 | 0.2706 | 6218 | a | Adenosine receptor activity, G-protein coupled |
| GO:0032230 | 2 | 2 | 2.45E-03 | 18 | 0.7562 | 178 | f | Positive regulation of synaptic transmission, GABAergic |
| GO:0048285 | 2 | 2 | 2.45E-03 | 18 | 0.5246 | 2625 | f | Organelle fission |
| GO:0007217 | 2 | 2 | 2.45E-03 | 18 | 0.8452 | 17 | a | Tachykinin signaling pathway |
| GO:0051319 | 2 | 2 | 2.45E-03 | 18 | 0.5124 | 2878 | f | G2-phase |
| GO:0015851 | 2 | 2 | 2.45E-03 | 18 | 0.3764 | 5103 | f | Nucleobase transport |
| GO:0016519 | 2 | 2 | 2.45E-03 | 18 | 0.1972 | 6600 | f | Gastric inhibitory peptide receptor activity |
| GO:0000085 | 2 | 2 | 2.45E-03 | 18 | 0.5650 | 1945 | f | G2-phase of mitotic cell cycle |
| GO:0016021 | 874 | 59 | 4.68E-03 | 31 | 0.8924 | 3 | a, b | Integral to membrane |
| GO:0005886 | 727 | 50 | 6.95E-03 | 36 | 0.8562 | 9 | a, b | Plasma membrane |
| GO:0004703 | 3 | 2 | 7.10E-03 | 40 | 0.8536 | 15 | c | G-protein-coupled receptor kinase activity |
| GO:0000030 | 4 | 2 | 1.37E-02 | 61 | 0.8556 | 11 | c | Mannosyltransferase activity |
| GO:0016758 | 41 | 6 | 1.45E-02 | 70 | 0.9004 | 1 | c | Transferase activity, transferring hexosyl groups |
| GO:0015020 | 5 | 2 | 2.22E-02 | 92 | 0.8538 | 14 | c | glucuronosyltransferase activity |
| GO:0045892 | 89 | 9 | 3.09E-02 | 104 | 0.8996 | 2 | d | Negative regulation of transcription, DNA dependent |
| GO:0015075 | 135 | 12 | 3.41E-02 | 115 | 0.8568 | 8 | b | Ion transmembrane transporter activity |
| GO:0003844 | 1 | 1 | 4.96E-02 | 281 | 0.8506 | 16 | c | 1,4-Alpha-glucan branching enzyme activity |
| GO:0022891 | 160 | 13 | 5.22E-02 | 289 | 0.8562 | 10 | b | Substrate -specific transmembrane transporter activity |
| GO:0042328 | 2 | 1 | 9.67E-02 | 471 | 0.8414 | 20 | c | Heparan sulfate N-acetylglucosaminyltransferase activity |
| GO:0000122 | 66 | 6 | 1.07E-01 | 491 | 0.8556 | 12 | d | Negative regulation of transcription from RNA polymerase II promoter |
| GO:0004674 | 200 | 14 | 1.18E-01 | 512 | 0.8550 | 13 | c | Protein serine/threonine kinase activity |
| GO:0008375 | 14 | 2 | 1.51E-01 | 620 | 0.8770 | 4 | c | Acetylglucosaminyltransferase activity |
| GO:0007186 | 101 | 7 | 2.33E-01 | 814 | 0.8430 | 19 | a | G-protein-coupled receptor protein signaling pathway |
| GO:0042629 | 2 | 0 | 1.0 | NA | 0.8432 | 18 | b | Mast cell granule |
The columns IA and nA represent the cardinality of the relevant GO term and the number of genes in the GO term that also appear in Gene Cluster #7; P-value and RankP represent the hypergeometric P-value computed by CLASSIFI, and the rank of the GO terms based on the P-value; and B-score and RankB represent the GO-Bayes measure and the corresponding rank of the GO terms. Under the column ‘Group’, ‘a’ represents GO terms closely related to GO:0007188 (G-protein signaling, coupled to cAMP nucleotide second messenger) in the GO hierarchy; ‘b’ represents GO terms closely related to GO:0005764 (lysosome); ‘c’ represents GO terms closely related to GO:0016757 (transferase activity, transferring glycosyl groups); ‘d’ represents GO terms closely related to GO:0045892 (negative regulation of transcription, DNA-dependent); and ‘f’ represents GO terms unrelated to the above four groups. NA, not applicable.