Table 7.
Estimating annotation quality using protein features and sequence data
| Organism | Domain score outlier | +,-,truncated domain | Length outlier | Conserved downstream Methionine | No protein in main cluster | Negative sum-of-logs score | Core proteins |
|---|---|---|---|---|---|---|---|
| *human |
0.000 |
0.021 |
0.017 |
0.028 |
0.012 |
10.256 |
7419 |
| *housemouse |
0.002 |
0.033 |
0.036 |
0.051 |
0.049 |
8.135 |
6811 |
| *dog |
0.005 |
0.068 |
0.115 |
0.051 |
0.030 |
7.268 |
6495 |
| *African savanna elephant |
0.006 |
0.096 |
0.163 |
0.038 |
0.042 |
6.816 |
5685 |
| *domestic guinea pig |
0.005 |
0.093 |
0.158 |
0.047 |
0.045 |
6.812 |
5699 |
| *cow |
0.008 |
0.082 |
0.101 |
0.041 |
0.060 |
6.795 |
6394 |
| pygmy chimpanzee |
0.003 |
0.100 |
0.146 |
0.081 |
0.044 |
6.764 |
6584 |
| *horse |
0.006 |
0.105 |
0.149 |
0.054 |
0.042 |
6.699 |
5838 |
| rabbit |
0.004 |
0.122 |
0.189 |
0.050 |
0.052 |
6.646 |
4159 |
| chimpanzee |
0.005 |
0.108 |
0.138 |
0.068 |
0.048 |
6.600 |
6455 |
| *norway rat |
0.008 |
0.077 |
0.084 |
0.061 |
0.080 |
6.600 |
5851 |
| giant panda |
0.005 |
0.139 |
0.224 |
0.063 |
0.035 |
6.501 |
5765 |
| olive baboon |
0.006 |
0.115 |
0.156 |
0.077 |
0.048 |
6.416 |
5872 |
| *bolivian squirrel monkey |
0.007 |
0.108 |
0.152 |
0.086 |
0.053 |
6.284 |
6035 |
| white-tufted-ear marmoset |
0.005 |
0.126 |
0.207 |
0.083 |
0.055 |
6.197 |
5777 |
| domestic cat |
0.005 |
0.193 |
0.254 |
0.070 |
0.041 |
6.178 |
6007 |
| northern white-cheeked gibbon |
0.006 |
0.148 |
0.195 |
0.077 |
0.056 |
6.151 |
5730 |
| western gorilla |
0.007 |
0.167 |
0.197 |
0.078 |
0.057 |
5.958 |
5722 |
| small-eared galago |
0.012 |
0.138 |
0.197 |
0.076 |
0.046 |
5.955 |
6128 |
| gray short-tailed opossum |
0.006 |
0.214 |
0.370 |
0.058 |
0.041 |
5.924 |
4500 |
| chinese hamster |
0.006 |
0.190 |
0.265 |
0.066 |
0.061 |
5.892 |
4901 |
| sheep |
0.007 |
0.232 |
0.292 |
0.070 |
0.041 |
5.871 |
5339 |
| *chicken |
0.013 |
0.175 |
0.228 |
0.072 |
0.051 |
5.729 |
3354 |
| rhesus macaque |
0.011 |
0.169 |
0.216 |
0.083 |
0.072 |
5.639 |
5466 |
| pig |
0.025 |
0.192 |
0.230 |
0.061 |
0.042 |
5.551 |
4616 |
| sumatran orangutan |
0.014 |
0.169 |
0.222 |
0.081 |
0.071 |
5.509 |
5050 |
| *green anole |
0.018 |
0.215 |
0.296 |
0.068 |
0.048 |
5.431 |
2797 |
| nile tilapia |
0.011 |
0.392 |
0.583 |
0.071 |
0.061 |
4.961 |
1296 |
| tasmanian devil |
0.016 |
0.337 |
0.478 |
0.082 |
0.054 |
4.933 |
3457 |
| *zebrafish |
0.025 |
0.344 |
0.464 |
0.062 |
0.068 |
4.773 |
1210 |
| torafugu |
0.017 |
0.448 |
0.601 |
0.060 |
0.063 |
4.765 |
1130 |
| turkey |
0.023 |
0.425 |
0.520 |
0.077 |
0.055 |
4.659 |
1821 |
| western clawed frog |
0.023 |
0.394 |
0.484 |
0.073 |
0.070 |
4.644 |
2268 |
| platypus |
0.031 |
0.435 |
0.586 |
0.068 |
0.067 |
4.451 |
1439 |
| Average |
0.010 |
0.187 |
0.256 |
0.066 |
0.052 |
6.111 |
4796 |
| Standard deviation |
0.008 |
0.120 |
0.160 |
0.014 |
0.014 |
1.114 |
1826 |
| Correlation Contig N50 |
−0.290 |
−0.337 |
−0.362 |
−0.489 |
−0.434 |
0.719 |
0.319 |
| Correlation EST count | −0.164 | −0.299 | −0.342 | −0.555 | −0.395 | 0.684 | 0.263 |
Columns 2–7 provide fraction of genes from each species in the orthology dataset and lacking conserved protein; outlier domain score; missing, extra, or truncated domain; outlier length; conserved downstream or upstream Met; and proteins not found in largest cluster. Column 8 provides the negative sum of logs score. The last column provides the number of genes in each species that are members of a “core” set defined as ortholog sets with members from at least 17 species that each have conserved splicing to at least 3 proteins from reference species (reference species are marked with *.)