Table 5 |
|||||||||
|
MisPred analysis of human genes predicted by the EnsEMBL and NCBI's GNOMON pipelines |
|||||||||
|
EnsEMBL |
|||||||||
|
|
|||||||||
|
Conflict 1 |
Number of proteins |
Identified as containing an extracellular domain |
Percentage |
Identified as suspicious by MisPred |
Percentage* |
False Positives |
Percentage* |
True errors |
Percentage* |
|
|
|||||||||
|
Homo sapiens |
2772 |
147 |
5.3% |
23 |
15.65% |
ND |
ND |
ND |
ND |
|
Monodelphis domestica |
10519 |
680 |
6.46% |
137 |
20.15% |
ND |
ND |
ND |
ND |
|
Gallus gallus |
6139 |
345 |
5.62% |
113 |
32.75% |
ND |
ND |
ND |
ND |
|
Danio rerio |
10289 |
860 |
8.36% |
317 |
36.86% |
ND |
ND |
ND |
ND |
|
|
|||||||||
|
Conflict 2 |
Number of proteins |
Identified as containing an extra- and an intracellular domain |
Percentage |
Identified as suspicious by MisPred |
Percentage* |
False Positives |
Percentage* |
True errors |
Percentage* |
|
|
|||||||||
|
Homo sapiens |
2772 |
1 |
0.04% |
0 |
0.00% |
0 |
0.00% |
0 |
0.00% |
|
Monodelphis domestica |
10519 |
10 |
0.1% |
0 |
0.00% |
0 |
0.00% |
0 |
0.00% |
|
Gallus gallus |
6139 |
2 |
0.03% |
0 |
0.00% |
0 |
0.00% |
0 |
0.00% |
|
Danio rerio |
10289 |
20 |
0.19% |
5 |
25% |
4 |
20% |
1 |
5% |
|
|
|||||||||
|
Conflict 3 |
Number of proteins |
Identified as suspicious by MisPred |
Percentage* |
False Positives |
Percentage* |
True errors |
Percentage* |
||
|
|
|
||||||||
|
Homo sapiens |
2772 |
0 |
0.00% |
0 |
0.00% |
0 |
0.00% |
||
|
Monodelphis domestica |
10519 |
0 |
0.00% |
0 |
0.00% |
0 |
0.00% |
||
|
Gallus gallus |
6139 |
0 |
0.00% |
0 |
0.00% |
0 |
0.00% |
||
|
Danio rerio |
10289 |
0 |
0.00% |
0 |
0.00% |
0 |
0.00% |
||
|
|
|||||||||
|
Conflict 4 |
Number of proteins |
Proteins containing domains suitable for the study of domain integrity |
Percentage |
Identified as suspicious by MisPred |
Percentage* |
False Positives |
Percentage* |
True errors |
Percentage* |
|
|
|||||||||
|
Homo sapiens |
2772 |
722 |
26.05% |
48 |
6.65% |
ND |
ND |
ND |
ND |
|
Monodelphis domestica |
10519 |
3726 |
35.42% |
119 |
3.19% |
ND |
ND |
ND |
ND |
|
Gallus gallus |
6139 |
1640 |
26.72% |
159 |
9.70% |
ND |
ND |
ND |
ND |
|
Danio rerio |
10289 |
2565 |
24.93% |
197 |
7.68% |
ND |
ND |
ND |
ND |
|
|
|||||||||
|
Conflict 5 |
Number of proteins |
Identified as suspicious by MisPred |
Percentage* |
False Positives |
Percentage* |
True errors |
Percentage* |
||
|
|
|
||||||||
|
Homo sapiens |
2772 |
0 |
0.00% |
0 |
0.00% |
0 |
0.00% |
||
|
Danio rerio |
10289 |
0 |
0.00% |
0 |
0.00% |
0 |
0.00% |
||
|
|
|||||||||
|
NCBI/GNOMON |
|||||||||
|
|
|||||||||
|
Conflict 1 |
Number of proteins |
Identified as containing an extracellular domain |
Percentage |
Identified as suspicious by MisPred |
Percentage* |
False Positives |
Percentage* |
True errors |
Percentage* |
|
|
|||||||||
|
Homo sapiens |
3012 |
139 |
4.61% |
32 |
23.02% |
ND |
ND |
ND |
ND |
|
Monodelphis domestica |
9703 |
642 |
6.62% |
112 |
17.45% |
ND |
ND |
ND |
ND |
|
Gallus gallus |
5604 |
310 |
5.53% |
88 |
28.39% |
ND |
ND |
ND |
ND |
|
Danio rerio |
8905 |
742 |
8.33% |
158 |
21.29% |
ND |
ND |
ND |
ND |
|
|
|||||||||
|
Conflict 2 |
Number of proteins |
Identified as containing an extra- and an intracellular domain |
Percentage |
Identified as suspicious by MisPred |
Percentage* |
False Positives |
Percentage* |
True errors |
Percentage* |
|
|
|||||||||
|
Homo sapiens |
3012 |
2 |
0.07% |
0 |
0% |
0 |
0.00% |
0 |
0.00% |
|
Monodelphis domestica |
9703 |
17 |
0.18% |
4 |
23.53% |
2 |
11.76% |
2 |
11.76% |
|
Gallus gallus |
5604 |
3 |
0.05% |
1 |
33.33% |
1 |
33.33% |
0 |
0.00% |
|
Danio rerio |
8905 |
16 |
0.18% |
6 |
37.5% |
4 |
25% |
2 |
12.5% |
|
|
|||||||||
|
Conflict 3 |
Number of proteins |
Identified as suspicious by MisPred |
Percentage* |
False Positives |
Percentage* |
True errors |
Percentage* |
||
|
|
|
||||||||
|
Homo sapiens |
3012 |
0 |
0.00% |
0 |
0.00% |
0 |
0.00% |
||
|
Monodelphis domestica |
9703 |
1 |
0.01% |
0 |
0.00% |
1 |
0.01% |
||
|
Gallus gallus |
5604 |
0 |
0.00% |
0 |
0.00% |
0 |
0.00% |
||
|
Danio rerio |
8905 |
2 |
0.02% |
1 |
0.01% |
1 |
0.01% |
||
|
|
|||||||||
|
Conflict 4 |
Number of proteins |
Proteins containing domains suitable for the study of domain integrity |
Percentage |
Identified as suspicious by MisPred |
Percentage* |
False Positives |
Percentage* |
True errors |
Percentage* |
|
|
|||||||||
|
Homo sapiens |
3012 |
792 |
26.3% |
41 |
5.18% |
ND |
ND |
ND |
ND |
|
Monodelphis domestica |
9703 |
3420 |
35.25% |
39 |
1.14% |
ND |
ND |
ND |
ND |
|
Gallus gallus |
5604 |
1500 |
26.77% |
208 |
13.87% |
ND |
ND |
ND |
ND |
|
Danio rerio |
8905 |
2059 |
23.12% |
300 |
14.57% |
ND |
ND |
ND |
ND |
|
|
|||||||||
|
Conflict 5 |
Number of proteins |
Identified as suspicious by MisPred |
Percentage* |
False Positives |
Percentage* |
True errors |
Percentage* |
||
|
|
|
||||||||
|
Homo sapiens |
3012 |
1 |
0.03% |
0 |
0.00% |
1 |
0.03% |
||
|
Danio rerio |
8905 |
5 |
0.06% |
5 |
0.06% |
0 |
0.00% |
||
|
|
|||||||||
|
*Values for suspicious, false positive and true positive sequences are expressed as percentage of the proteins relevant for the given conflict. ND – not determined. The data refer to human genes for which both gene prediction pipelines generated at least one gene model. |
|||||||||
|
Nagy et al. BMC Bioinformatics 2008 9:353 doi:10.1186/1471-2105-9-353 |
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