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Table 2 Comparison of GO mapping classification to Valle's categories

From: Evaluation of high-throughput functional categorization of human disease genes

Valle's Category Original curation HDG count True Positives False Negatives False Positives GO-Mapping precision GO-Mapping recall
Cell Signalling 20 11 9 20 35% 55%
Channel 32 25 7 15 61% 78%
Enzyme 232 208 24 107 66% 90%
Extracellular matrix component 54 41 13 25 62% 76%
Hormone 14 14 0 1 93% 100%
Immunoglobulin 4 1 3 2 33% 25%
Intracellular matrix component 50 23 27 207 10% 46%
Modulator of protein function 105 4 101 5 44% 4%
Receptor 86 82 4 96 46% 95%
Transcription factor 79 62 17 10 85% 78%
Transmembrane Transporter 35 42 3 102 29% 93%
Totals & overall accuracy scores 711 513 208 590* 47%** 71%**
  1. * Due to the possible assignment of more than one GO term per gene, we overestimated the overall FP rate as one gene classified multiple times due to multiple GO annotations lead to counting as a FP the same gene more than once.
  2. ** Overall accuracy scores are calculated from the overall True positive, false positive and false negative scores (they are not an average of the categorical accuracy scores)