Table 1.
Selected gene ontology (GO) categories of vertebrate genes overlapped by highly conserved elements
| CDS
|
5′ UTR
|
3′ UTR
|
Intron
|
|||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Term | Description | Na | exp.b | obs.c | Pd | exp. | obs. | P | exp. | obs. | P | exp. | obs. | P |
| GO:0003677 | DNA binding | 1914 | 164.5 | 378 | 1.3e-62 | 59.4 | 158 | 1.5e-33 | 84.4 | 221 | 1.0e-45 | 28.6 | 80 | 5.1e-19 |
| GO:0030528 | transcription regulator activity | 1125 | 96.7 | 251 | 1.7e-49 | 34.9 | 119 | 2.4e-34 | 49.6 | 140 | 8.5e-31 | 16.8 | 54 | 6.2e-15 |
| GO:0007275 | development | 1746 | 150.1 | 266 | 1.2e-22 | 54.2 | 115 | 1.0e-15 | 77.0 | 122 | 1.1e-07 | 26.0 | 47 | 3.8e-05 |
| GO:0005216 | ion channel activity | 334 | 28.7 | 79 | 3.8e-17 | 10.3 | 24 | 1.2e-04 | 14.7 | 16 | 4.0e-01 | 4.9 | 2 | 1.2e-01 |
| GO:0006333 | chromatin assembly/disassembly | 153 | 13.1 | 47 | 3.1e-15 | 4.7 | 11 | 8.3e-03 | 6.7 | 17 | 4.2e-04 | 2.2 | 2 | 6.0e-01 |
| GO:0007399 | neurogenesis | 384 | 33.0 | 82 | 5.2e-15 | 11.9 | 38 | 2.7e-10 | 16.9 | 36 | 1.7e-05 | 5.7 | 15 | 6.7e-04 |
| GO:0009887 | organogenesis | 880 | 75.6 | 144 | 1.0e-14 | 27.3 | 67 | 6.2e-12 | 38.8 | 64 | 5.2e-05 | 13.1 | 27 | 3.0e-04 |
| GO:0009653 | morphogenesis | 1099 | 94.4 | 169 | 1.3e-14 | 34.1 | 76 | 2.2e-11 | 48.5 | 77 | 3.1e-05 | 16.4 | 34 | 3.8e-05 |
| GO:0008066 | glutamate receptor activity | 38 | 3.2 | 19 | 3.6e-11 | 1.1 | 6 | 1.0e-03 | 1.6 | 5 | 2.5e-02 | – | – | – |
| GO:0008134 | transcription factor binding | 251 | 21.5 | 54 | 1.9e-10 | 7.7 | 21 | 3.8e-05 | 11.0 | 35 | 1.5e-09 | 3.7 | 10 | 4.5e-03 |
| GO:0005515 | protein binding | 2179 | 187.3 | 252 | 1.4e-07 | 67.7 | 98 | 6.9e-05 | 96.1 | 141 | 8.9e-07 | 32.5 | 41 | 6.7e-02 |
| GO:0007018 | microtubule-based movement | 55 | 4.7 | 18 | 3.9e-07 | – | – | – | 2.4 | 8 | 2.6e-03 | 0.8 | 2 | 2.0e-01 |
| GO:0003723 | RNA binding | 601 | 51.6 | 88 | 4.2e-07 | 18.6 | 26 | 5.6e-02 | 26.5 | 66 | 5.5e-12 | 8.9 | 7 | 3.2e-01 |
| GO:0007268 | synaptic transmission | 240 | 20.6 | 44 | 1.1e-06 | 7.4 | 12 | 7.2e-02 | 10.5 | 10 | 5.1e-01 | – | – | – |
| GO:0030154 | cell differentiation | 200 | 17.1 | 37 | 6.4e-06 | 6.2 | 17 | 1.7e-04 | 8.8 | 15 | 3.2e-02 | 2.9 | 7 | 3.1e-02 |
| GO:0007267 | cell-cell signaling | 532 | 45.7 | 77 | 3.5e-06 | 16.5 | 23 | 6.9e-02 | 23.4 | 24 | 4.9e-01 | 7.9 | 2 | 1.3e-02 |
| GO:0016071 | mRNA metabolism | 188 | 16.1 | 35 | 9.8e-06 | 5.8 | 10 | 6.9e-02 | 8.2 | 29 | 3.7e-09 | 2.8 | 3 | 5.4e-01 |
| GO:0006397 | mRNA processing | 170 | 14.6 | 30 | 1.2e-04 | 5.2 | 8 | 1.6e-01 | 7.5 | 24 | 4.5e-07 | 2.5 | 3 | 4.7e-01 |
| GO:0006512 | ubiquitin cycle | 542 | 46.6 | 69 | 5.9e-04 | 16.8 | 22 | 1.2e-01 | 23.9 | 45 | 3.4e-05 | 8.1 | 3 | 3.6e-02 |
a
Number of genes in background set assigned to category.
b
Expected number of genes overlapped under background distribution.
c
Observed number of genes overlapped.
d
P-value. Values of less than 5e-5 can be considered significant (see Methods).