Table 7 Time in seconds to measure gene functional similarity of five organisms
From: SGFSC: speeding the gene functional similarity calculation based on hash tables
Organism | Type | # of annotated genes | # of average annotations | # of gene pairs | Time Resnik | Time Jiang | Time Lin | Time Wang | Time Pekar | Time simUI | Time simGIC |
|---|---|---|---|---|---|---|---|---|---|---|---|
Human | BP | 39337 | 4.35 | 7.74 × 108 | 36702 | 36487 | 36366 | 36427 | 36972 | 19088 | 19762 |
|  | CC | 35975 | 2.56 | 6.47 × 108 | 5843 | 5815 | 5814 | 5810 | 5869 | 4921 | 5815 |
|  | MF | 38404 | 2.32 | 7.37 × 108 | 323 | 326 | 327 | 321 | 326 | 4519 | 4828 |
Arabidopsis | BP | 25532 | 3.24 | 3.26 × 108 | 6945 | 6957 | 5948 | 6956 | 6953 | 5238 | 5590 |
|  | CC | 17683 | 2.00 | 1.56 × 108 | 812 | 808 | 841 | 816 | 816 | 962 | 989 |
|  | MF | 20305 | 1.92 | 2.06 × 108 | 632 | 616 | 619 | 622 | 628 | 1048 | 1091 |
Yeast | BP | 5906 | 3.20 | 1.74 × 107 | 578 | 580 | 586 | 583 | 579 | 353 | 383 |
|  | CC | 5660 | 2.22 | 1.60 × 107 | 143 | 146 | 145 | 146 | 144 | 432 | 142 |
|  | MF | 5902 | 2.30 | 1.74 × 107 | 66 | 64 | 66 | 65 | 64 | 94 | 100 |
Rat | BP | 23319 | 4.62 | 2.65 × 108 | 13650 | 13690 | 13641 | 13714 | 13705 | 7219 | 7954 |
|  | CC | 22217 | 2.60 | 2.47 × 108 | 2319 | 2314 | 2299 | 2411 | 2319 | 1911 | 2083 |
|  | MF | 23065 | 2.49 | 2.66 × 108 | 1334 | 1315 | 1351 | 1339 | 1330 | 1750 | 1874 |
Oryza | BP | 1909 | 1.44 | 1.82 × 106 | 8 | 8 | 7 | 8 | 8 | 13 | 13 |
|  | CC | 39995 | 1.06 | 8.00 × 108 | 1262 | 1343 | 1307 | 1258 | 1254 | 2976 | 3115 |
|  | MF | 2041 | 1.60 | 2.08 × 106 | 5 | 5 | 5 | 4 | 5 | 9 | 10 |