| (A) Differential alternative splicing . | ||||
|---|---|---|---|---|
| GO . | Hooks . | Hooks (FET) . | Wagner . | Wagner (FET) . |
| Small molecule metabolic process (GO:0044281) | 157/895 (17.5%) versus 1396/15 806 (8.8%) | 4.5 |$\times$|−14 | 195/1183 (16.5%) versus 1654/18 943 (8.7%) | 2.6 |$\times$|−15 |
| Carboxylic acid metabolic process (GO:0019752) | 99/895 (11.1%) versus 724/15 803 (4.6%) | 4.73|$ \times$|10−13 | 129/1183 (10.9%) versus 861/18 940 (4.5%) | 2.31|$ \times$|10−17 |
| Organic acid metabolic process (GO:0006082) | 101/895 (11.3%) versus 752/15 803 (4.8%) | 7.72|$ \times$|10−13 | 135/1183 (11.4%) versus 892/18 940 (4.7%) | 9.88|$ \times$|10−19 |
| Oxoacid metabolic process (GO:0043436) | 100/895 (11.2%) versus 745/15 803 (4.7%) | 1.15|$ \times$|10−12 | 134/1183 (11.3%) versus 886/18 940 (4.7%) | 1.53|$ \times$|10−18 |
| Lipid metabolic process (GO:0006629) | 110/895 (12.3%) versus 899/15 803 (5.7%) | 2.47|$ \times$|10−11 | 138/1183 (11.7%) versus 1127/18 940 (6.0%) | 4.02|$ \times$|10−11 |
| Monocarboxylic acid metabolic process (GO:0032787) | 65/895 (7.3%) versus 435/15 803 (2.8%) | 1.97|$ \times$|10−9 | 86/1183 (7.3%) versus 501/18 940 (2.6%) | 2.97|$ \times$|10−14 |
| Carboxylic acid catabolic process (GO:0046395) | 42/895 (4.7%) versus 224/15 803 (1.4%) | 1.88|$ \times$|10−8 | 51/1183 (4.3%) versus 281/18 940 (1.5%) | 2.17|$ \times$|10−8 |
| Organic acid catabolic process (GO:0016054) | 42/895 (4.7%) versus 224/15 803 (1.4%) | 1.88|$ \times$|10−8 | 51/1183 (4.3%) versus 281/18 940 (1.5%) | 2.17|$ \times$|10−8 |
| Small molecule catabolic process (GO:0044282) | 50/895 (5.6%) versus 303/15 803 (1.9%) | 2.61|$ \times$|10−8 | 61/1183 (5.2%) versus 377/18 940 (2.0%) | 3.02|$ \times$|10−8 |
| Cellular lipid metabolic process (GO:0044255) | 83/895 (9.3%) versus 690/15 803 (4.4%) | 1.66|$ \times$|10−7 | 106/1183 (9.0%) versus 877/18 940 (4.6%) | 1.51|$ \times$|10−7 |
| (B) Differential gene expression | ||||
| GO | Hooks | Hooks (FET) | Wagner | Wagner (FET) |
| Small molecule metabolic process (GO:0044281) | 409/1957 (20.9%) versus 848/7696 (11.0%) | 9.80|$ \times$|10−49 | 299/1400 (21.4%) versus 956/8661 (11.0%) | 1.08|$ \times$|10−31 |
| Organic acid metabolic process (GO:0006082) | 251/1957 (12.8%) versus 454/7696 (5.9%) | 1.22|$ \times$|10−40 | 187/1400 (13.4%) versus 515/8661 (5.9%) | 6.83|$ \times$|10−27 |
| Oxoacid metabolic process (GO:0043436) | 249/1957 (12.7%) versus 450/7696 (5.8%) | 2.30|$ \times$|10−40 | 186/1400 (13.3%) versus 511/8661 (5.9%) | 6.99|$ \times$|10−27 |
| Carboxylic acid metabolic process (GO:0019752) | 242/1957 (12.4%) versus 439/7696 (5.7%) | 1.06|$ \times$|10−38 | 181/1400 (12.9%) versus 499/8661 (5.8%) | 7.99|$ \times$|10−26 |
| Small molecule catabolic process (GO:0 044 282) | 130/1957 (6.6%) versus 199/7696 (2.6%) | 2.86|$ \times$|10−29 | 99/1400 (7.1%) versus 231/8661 (2.7%) | 1.01|$ \times$|10−18 |
| Monocarboxylic acid metabolic process (GO:0032787) | 154/1957 (7.9%) versus 263/7696 (3.4%) | 3.52|$ \times$|10−27 | 118/1400 (8.4%) versus 300/8661 (3.5%) | 5.16|$ \times$|10−19 |
| Carboxylic acid catabolic process (GO:0046395) | 102/1957 (5.2%) versus 144/7696 (1.9%) | 8.06|$ \times$|10−27 | 81/1400 (5.8%) versus 167/8661 (1.9%) | 5.15|$ \times$|10−19 |
| Organic acid catabolic process (GO:0016054) | 102/1957 (5.2%) versus 144/7696 (1.9%) | 8.06|$ \times$|10−27 | 81/1400 (5.8%) versus 167/8661 (1.9%) | 5.15|$ \times$|10−19 |
| Lipid metabolic process (GO:0006629) | 260/1957 (13.3%) versus 563/7696 (7.3%) | 8.88|$ \times$|10−25 | 194/1400 (13.9%) versus 662/8661 (7.6%) | 4.05|$ \times$|10−15 |
| Oxidoreductase activity (GO:0016491) | 183/1957 (9.4%) versus 356/7696 (4.6%) | 3.69|$ \times$|10−23 | 128/1400 (9.1%) versus 396/8661 (4.6%) | 1.89|$ \times$|10−12 |
| (A) Differential alternative splicing . | ||||
|---|---|---|---|---|
| GO . | Hooks . | Hooks (FET) . | Wagner . | Wagner (FET) . |
| Small molecule metabolic process (GO:0044281) | 157/895 (17.5%) versus 1396/15 806 (8.8%) | 4.5 |$\times$|−14 | 195/1183 (16.5%) versus 1654/18 943 (8.7%) | 2.6 |$\times$|−15 |
| Carboxylic acid metabolic process (GO:0019752) | 99/895 (11.1%) versus 724/15 803 (4.6%) | 4.73|$ \times$|10−13 | 129/1183 (10.9%) versus 861/18 940 (4.5%) | 2.31|$ \times$|10−17 |
| Organic acid metabolic process (GO:0006082) | 101/895 (11.3%) versus 752/15 803 (4.8%) | 7.72|$ \times$|10−13 | 135/1183 (11.4%) versus 892/18 940 (4.7%) | 9.88|$ \times$|10−19 |
| Oxoacid metabolic process (GO:0043436) | 100/895 (11.2%) versus 745/15 803 (4.7%) | 1.15|$ \times$|10−12 | 134/1183 (11.3%) versus 886/18 940 (4.7%) | 1.53|$ \times$|10−18 |
| Lipid metabolic process (GO:0006629) | 110/895 (12.3%) versus 899/15 803 (5.7%) | 2.47|$ \times$|10−11 | 138/1183 (11.7%) versus 1127/18 940 (6.0%) | 4.02|$ \times$|10−11 |
| Monocarboxylic acid metabolic process (GO:0032787) | 65/895 (7.3%) versus 435/15 803 (2.8%) | 1.97|$ \times$|10−9 | 86/1183 (7.3%) versus 501/18 940 (2.6%) | 2.97|$ \times$|10−14 |
| Carboxylic acid catabolic process (GO:0046395) | 42/895 (4.7%) versus 224/15 803 (1.4%) | 1.88|$ \times$|10−8 | 51/1183 (4.3%) versus 281/18 940 (1.5%) | 2.17|$ \times$|10−8 |
| Organic acid catabolic process (GO:0016054) | 42/895 (4.7%) versus 224/15 803 (1.4%) | 1.88|$ \times$|10−8 | 51/1183 (4.3%) versus 281/18 940 (1.5%) | 2.17|$ \times$|10−8 |
| Small molecule catabolic process (GO:0044282) | 50/895 (5.6%) versus 303/15 803 (1.9%) | 2.61|$ \times$|10−8 | 61/1183 (5.2%) versus 377/18 940 (2.0%) | 3.02|$ \times$|10−8 |
| Cellular lipid metabolic process (GO:0044255) | 83/895 (9.3%) versus 690/15 803 (4.4%) | 1.66|$ \times$|10−7 | 106/1183 (9.0%) versus 877/18 940 (4.6%) | 1.51|$ \times$|10−7 |
| (B) Differential gene expression | ||||
| GO | Hooks | Hooks (FET) | Wagner | Wagner (FET) |
| Small molecule metabolic process (GO:0044281) | 409/1957 (20.9%) versus 848/7696 (11.0%) | 9.80|$ \times$|10−49 | 299/1400 (21.4%) versus 956/8661 (11.0%) | 1.08|$ \times$|10−31 |
| Organic acid metabolic process (GO:0006082) | 251/1957 (12.8%) versus 454/7696 (5.9%) | 1.22|$ \times$|10−40 | 187/1400 (13.4%) versus 515/8661 (5.9%) | 6.83|$ \times$|10−27 |
| Oxoacid metabolic process (GO:0043436) | 249/1957 (12.7%) versus 450/7696 (5.8%) | 2.30|$ \times$|10−40 | 186/1400 (13.3%) versus 511/8661 (5.9%) | 6.99|$ \times$|10−27 |
| Carboxylic acid metabolic process (GO:0019752) | 242/1957 (12.4%) versus 439/7696 (5.7%) | 1.06|$ \times$|10−38 | 181/1400 (12.9%) versus 499/8661 (5.8%) | 7.99|$ \times$|10−26 |
| Small molecule catabolic process (GO:0 044 282) | 130/1957 (6.6%) versus 199/7696 (2.6%) | 2.86|$ \times$|10−29 | 99/1400 (7.1%) versus 231/8661 (2.7%) | 1.01|$ \times$|10−18 |
| Monocarboxylic acid metabolic process (GO:0032787) | 154/1957 (7.9%) versus 263/7696 (3.4%) | 3.52|$ \times$|10−27 | 118/1400 (8.4%) versus 300/8661 (3.5%) | 5.16|$ \times$|10−19 |
| Carboxylic acid catabolic process (GO:0046395) | 102/1957 (5.2%) versus 144/7696 (1.9%) | 8.06|$ \times$|10−27 | 81/1400 (5.8%) versus 167/8661 (1.9%) | 5.15|$ \times$|10−19 |
| Organic acid catabolic process (GO:0016054) | 102/1957 (5.2%) versus 144/7696 (1.9%) | 8.06|$ \times$|10−27 | 81/1400 (5.8%) versus 167/8661 (1.9%) | 5.15|$ \times$|10−19 |
| Lipid metabolic process (GO:0006629) | 260/1957 (13.3%) versus 563/7696 (7.3%) | 8.88|$ \times$|10−25 | 194/1400 (13.9%) versus 662/8661 (7.6%) | 4.05|$ \times$|10−15 |
| Oxidoreductase activity (GO:0016491) | 183/1957 (9.4%) versus 356/7696 (4.6%) | 3.69|$ \times$|10−23 | 128/1400 (9.1%) versus 396/8661 (4.6%) | 1.89|$ \times$|10−12 |
Isopret analysis was performed as described on two RNA-seq datasets that compared hepatoblastoma to normal liver tissues. The panels show the GO terms that appeared in the top 10 annotations for both datasets. (A) For differential splicing, six terms were common to both datasets. (B) For differential gene expression, nine terms were common to both datasets. In this case, there was substantial overlap between overrepresented terms for expression and slicing, but in many cases, the overlap was much less (Supplementary Figure S2). FET: Fisher’s exact test.
| (A) Differential alternative splicing . | ||||
|---|---|---|---|---|
| GO . | Hooks . | Hooks (FET) . | Wagner . | Wagner (FET) . |
| Small molecule metabolic process (GO:0044281) | 157/895 (17.5%) versus 1396/15 806 (8.8%) | 4.5 |$\times$|−14 | 195/1183 (16.5%) versus 1654/18 943 (8.7%) | 2.6 |$\times$|−15 |
| Carboxylic acid metabolic process (GO:0019752) | 99/895 (11.1%) versus 724/15 803 (4.6%) | 4.73|$ \times$|10−13 | 129/1183 (10.9%) versus 861/18 940 (4.5%) | 2.31|$ \times$|10−17 |
| Organic acid metabolic process (GO:0006082) | 101/895 (11.3%) versus 752/15 803 (4.8%) | 7.72|$ \times$|10−13 | 135/1183 (11.4%) versus 892/18 940 (4.7%) | 9.88|$ \times$|10−19 |
| Oxoacid metabolic process (GO:0043436) | 100/895 (11.2%) versus 745/15 803 (4.7%) | 1.15|$ \times$|10−12 | 134/1183 (11.3%) versus 886/18 940 (4.7%) | 1.53|$ \times$|10−18 |
| Lipid metabolic process (GO:0006629) | 110/895 (12.3%) versus 899/15 803 (5.7%) | 2.47|$ \times$|10−11 | 138/1183 (11.7%) versus 1127/18 940 (6.0%) | 4.02|$ \times$|10−11 |
| Monocarboxylic acid metabolic process (GO:0032787) | 65/895 (7.3%) versus 435/15 803 (2.8%) | 1.97|$ \times$|10−9 | 86/1183 (7.3%) versus 501/18 940 (2.6%) | 2.97|$ \times$|10−14 |
| Carboxylic acid catabolic process (GO:0046395) | 42/895 (4.7%) versus 224/15 803 (1.4%) | 1.88|$ \times$|10−8 | 51/1183 (4.3%) versus 281/18 940 (1.5%) | 2.17|$ \times$|10−8 |
| Organic acid catabolic process (GO:0016054) | 42/895 (4.7%) versus 224/15 803 (1.4%) | 1.88|$ \times$|10−8 | 51/1183 (4.3%) versus 281/18 940 (1.5%) | 2.17|$ \times$|10−8 |
| Small molecule catabolic process (GO:0044282) | 50/895 (5.6%) versus 303/15 803 (1.9%) | 2.61|$ \times$|10−8 | 61/1183 (5.2%) versus 377/18 940 (2.0%) | 3.02|$ \times$|10−8 |
| Cellular lipid metabolic process (GO:0044255) | 83/895 (9.3%) versus 690/15 803 (4.4%) | 1.66|$ \times$|10−7 | 106/1183 (9.0%) versus 877/18 940 (4.6%) | 1.51|$ \times$|10−7 |
| (B) Differential gene expression | ||||
| GO | Hooks | Hooks (FET) | Wagner | Wagner (FET) |
| Small molecule metabolic process (GO:0044281) | 409/1957 (20.9%) versus 848/7696 (11.0%) | 9.80|$ \times$|10−49 | 299/1400 (21.4%) versus 956/8661 (11.0%) | 1.08|$ \times$|10−31 |
| Organic acid metabolic process (GO:0006082) | 251/1957 (12.8%) versus 454/7696 (5.9%) | 1.22|$ \times$|10−40 | 187/1400 (13.4%) versus 515/8661 (5.9%) | 6.83|$ \times$|10−27 |
| Oxoacid metabolic process (GO:0043436) | 249/1957 (12.7%) versus 450/7696 (5.8%) | 2.30|$ \times$|10−40 | 186/1400 (13.3%) versus 511/8661 (5.9%) | 6.99|$ \times$|10−27 |
| Carboxylic acid metabolic process (GO:0019752) | 242/1957 (12.4%) versus 439/7696 (5.7%) | 1.06|$ \times$|10−38 | 181/1400 (12.9%) versus 499/8661 (5.8%) | 7.99|$ \times$|10−26 |
| Small molecule catabolic process (GO:0 044 282) | 130/1957 (6.6%) versus 199/7696 (2.6%) | 2.86|$ \times$|10−29 | 99/1400 (7.1%) versus 231/8661 (2.7%) | 1.01|$ \times$|10−18 |
| Monocarboxylic acid metabolic process (GO:0032787) | 154/1957 (7.9%) versus 263/7696 (3.4%) | 3.52|$ \times$|10−27 | 118/1400 (8.4%) versus 300/8661 (3.5%) | 5.16|$ \times$|10−19 |
| Carboxylic acid catabolic process (GO:0046395) | 102/1957 (5.2%) versus 144/7696 (1.9%) | 8.06|$ \times$|10−27 | 81/1400 (5.8%) versus 167/8661 (1.9%) | 5.15|$ \times$|10−19 |
| Organic acid catabolic process (GO:0016054) | 102/1957 (5.2%) versus 144/7696 (1.9%) | 8.06|$ \times$|10−27 | 81/1400 (5.8%) versus 167/8661 (1.9%) | 5.15|$ \times$|10−19 |
| Lipid metabolic process (GO:0006629) | 260/1957 (13.3%) versus 563/7696 (7.3%) | 8.88|$ \times$|10−25 | 194/1400 (13.9%) versus 662/8661 (7.6%) | 4.05|$ \times$|10−15 |
| Oxidoreductase activity (GO:0016491) | 183/1957 (9.4%) versus 356/7696 (4.6%) | 3.69|$ \times$|10−23 | 128/1400 (9.1%) versus 396/8661 (4.6%) | 1.89|$ \times$|10−12 |
| (A) Differential alternative splicing . | ||||
|---|---|---|---|---|
| GO . | Hooks . | Hooks (FET) . | Wagner . | Wagner (FET) . |
| Small molecule metabolic process (GO:0044281) | 157/895 (17.5%) versus 1396/15 806 (8.8%) | 4.5 |$\times$|−14 | 195/1183 (16.5%) versus 1654/18 943 (8.7%) | 2.6 |$\times$|−15 |
| Carboxylic acid metabolic process (GO:0019752) | 99/895 (11.1%) versus 724/15 803 (4.6%) | 4.73|$ \times$|10−13 | 129/1183 (10.9%) versus 861/18 940 (4.5%) | 2.31|$ \times$|10−17 |
| Organic acid metabolic process (GO:0006082) | 101/895 (11.3%) versus 752/15 803 (4.8%) | 7.72|$ \times$|10−13 | 135/1183 (11.4%) versus 892/18 940 (4.7%) | 9.88|$ \times$|10−19 |
| Oxoacid metabolic process (GO:0043436) | 100/895 (11.2%) versus 745/15 803 (4.7%) | 1.15|$ \times$|10−12 | 134/1183 (11.3%) versus 886/18 940 (4.7%) | 1.53|$ \times$|10−18 |
| Lipid metabolic process (GO:0006629) | 110/895 (12.3%) versus 899/15 803 (5.7%) | 2.47|$ \times$|10−11 | 138/1183 (11.7%) versus 1127/18 940 (6.0%) | 4.02|$ \times$|10−11 |
| Monocarboxylic acid metabolic process (GO:0032787) | 65/895 (7.3%) versus 435/15 803 (2.8%) | 1.97|$ \times$|10−9 | 86/1183 (7.3%) versus 501/18 940 (2.6%) | 2.97|$ \times$|10−14 |
| Carboxylic acid catabolic process (GO:0046395) | 42/895 (4.7%) versus 224/15 803 (1.4%) | 1.88|$ \times$|10−8 | 51/1183 (4.3%) versus 281/18 940 (1.5%) | 2.17|$ \times$|10−8 |
| Organic acid catabolic process (GO:0016054) | 42/895 (4.7%) versus 224/15 803 (1.4%) | 1.88|$ \times$|10−8 | 51/1183 (4.3%) versus 281/18 940 (1.5%) | 2.17|$ \times$|10−8 |
| Small molecule catabolic process (GO:0044282) | 50/895 (5.6%) versus 303/15 803 (1.9%) | 2.61|$ \times$|10−8 | 61/1183 (5.2%) versus 377/18 940 (2.0%) | 3.02|$ \times$|10−8 |
| Cellular lipid metabolic process (GO:0044255) | 83/895 (9.3%) versus 690/15 803 (4.4%) | 1.66|$ \times$|10−7 | 106/1183 (9.0%) versus 877/18 940 (4.6%) | 1.51|$ \times$|10−7 |
| (B) Differential gene expression | ||||
| GO | Hooks | Hooks (FET) | Wagner | Wagner (FET) |
| Small molecule metabolic process (GO:0044281) | 409/1957 (20.9%) versus 848/7696 (11.0%) | 9.80|$ \times$|10−49 | 299/1400 (21.4%) versus 956/8661 (11.0%) | 1.08|$ \times$|10−31 |
| Organic acid metabolic process (GO:0006082) | 251/1957 (12.8%) versus 454/7696 (5.9%) | 1.22|$ \times$|10−40 | 187/1400 (13.4%) versus 515/8661 (5.9%) | 6.83|$ \times$|10−27 |
| Oxoacid metabolic process (GO:0043436) | 249/1957 (12.7%) versus 450/7696 (5.8%) | 2.30|$ \times$|10−40 | 186/1400 (13.3%) versus 511/8661 (5.9%) | 6.99|$ \times$|10−27 |
| Carboxylic acid metabolic process (GO:0019752) | 242/1957 (12.4%) versus 439/7696 (5.7%) | 1.06|$ \times$|10−38 | 181/1400 (12.9%) versus 499/8661 (5.8%) | 7.99|$ \times$|10−26 |
| Small molecule catabolic process (GO:0 044 282) | 130/1957 (6.6%) versus 199/7696 (2.6%) | 2.86|$ \times$|10−29 | 99/1400 (7.1%) versus 231/8661 (2.7%) | 1.01|$ \times$|10−18 |
| Monocarboxylic acid metabolic process (GO:0032787) | 154/1957 (7.9%) versus 263/7696 (3.4%) | 3.52|$ \times$|10−27 | 118/1400 (8.4%) versus 300/8661 (3.5%) | 5.16|$ \times$|10−19 |
| Carboxylic acid catabolic process (GO:0046395) | 102/1957 (5.2%) versus 144/7696 (1.9%) | 8.06|$ \times$|10−27 | 81/1400 (5.8%) versus 167/8661 (1.9%) | 5.15|$ \times$|10−19 |
| Organic acid catabolic process (GO:0016054) | 102/1957 (5.2%) versus 144/7696 (1.9%) | 8.06|$ \times$|10−27 | 81/1400 (5.8%) versus 167/8661 (1.9%) | 5.15|$ \times$|10−19 |
| Lipid metabolic process (GO:0006629) | 260/1957 (13.3%) versus 563/7696 (7.3%) | 8.88|$ \times$|10−25 | 194/1400 (13.9%) versus 662/8661 (7.6%) | 4.05|$ \times$|10−15 |
| Oxidoreductase activity (GO:0016491) | 183/1957 (9.4%) versus 356/7696 (4.6%) | 3.69|$ \times$|10−23 | 128/1400 (9.1%) versus 396/8661 (4.6%) | 1.89|$ \times$|10−12 |
Isopret analysis was performed as described on two RNA-seq datasets that compared hepatoblastoma to normal liver tissues. The panels show the GO terms that appeared in the top 10 annotations for both datasets. (A) For differential splicing, six terms were common to both datasets. (B) For differential gene expression, nine terms were common to both datasets. In this case, there was substantial overlap between overrepresented terms for expression and slicing, but in many cases, the overlap was much less (Supplementary Figure S2). FET: Fisher’s exact test.
This PDF is available to Subscribers Only
View Article Abstract & Purchase OptionsFor full access to this pdf, sign in to an existing account, or purchase an annual subscription.
