Table 4.
Gene Ontology terms disproportionately associated with different types of polyadenylation configuration
| GO termsa | Typeb | H.sapiens | M.musculus |
|---|---|---|---|
| Biological process | |||
| GO:0007166 (cell surface receptor linked site transduction) | I | 1.15E−04 (171, 37, 3) | 9.38E−06 (154, 30, 1) |
| GO:0046907 (intracellular transport) | II and III | 1.29E−07 (60, 59, 7) | 1.57E−08 (64, 68, 5) |
| GO:0015031 (protein transport) | 1.41E−07 (49, 53, 5) | 1.53E−07 (54, 59, 3) | |
| GO:0006886 (intracellular protein transport)c | 7.25E−08 (46, 52, 5) | 5.95E−07 (51, 55, 3) | |
| Cellular component | |||
| GO:0005576 (extracellular) | I | 9.98E−05 (168, 32, 8) | 2.54E−10 (518, 115, 24) |
| GO:0005622 (intracellular) | II and III | 6.32E−08 (819, 337, 109) | 1.62E−04 (826, 335, 92) |
| GO:0005524 (nucleus) | III | 7.84E−05 (393, 162, 66) | 2.50E−04 (376, 143, 53) |
| Molecular function | |||
| GO:0004871 (site transducer activity) | I | 4.94E−06 (344, 77, 18) | 3.81E−06 (315, 71, 13) |
| GO:0008565 (protein transporter activity) | II and III | 4.52E−07 (30, 42, 1) | 3.41E−07 (25, 40, 0) |
| GO:0003723 (RNA binding) | III | 1.17E−05 (46, 32, 19) | 1.12E−04 (40, 22, 14) |
aFor each GO term, its GO ID and annotation (in parentheses) are given.
bType is the type of polyadenylation configuration (shown in Figure 1B).
cGO:0006886 (intracellular protein transport) is associated with both GO:0046907 (intracellular transport) and GO:0015031 (protein transport) through an ‘is a’ relationship (for details see Materials and Methods). Three categories of GO (Biological Process, Cellular Component and Molecular Function) were studied to find correlation with polyadenylation configuration. For each GO term in one species, a P-value from Fisher's exact test is provided, which indicates the significance of the association between this GO term and polyadenylation configuration, i.e. the lower the P-value the more significant the association is. Multiple testing adjustment using the Benjamanini and Hochberg method was applied to the selection of significant GO terms. The numbers of genes in three polyadenylation configurations, i.e. type I, II and III, are listed in parentheses. For example, (171, 37, 3) means that 171 type I genes, 37 type II genes and 3 type III genes.