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Table 5 MisPred analysis of human genes predicted by the EnsEMBL and NCBI's GNOMON pipelines

From: Identification and correction of abnormal, incomplete and mispredicted proteins in public databases

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%
  1. *Values for suspicious, false positive and true positive sequences are expressed as percentage of the proteins relevant for the given conflict.
  2. ND – not determined.
  3. The data refer to human genes for which both gene prediction pipelines generated at least one gene model.