Type of evidence Low Confidence Medium Confidence High Confidence   MTB MLP MSM MTB MLP MSM MTB MLP MSM Genomic neighbourhood 1163 417 402 6972 1698 1661 4731 1237 836 Gene fusion 337 26 86 52 14 16 99 27 6 Co-occurence 1033 197 316 5862 276 932 1461 120 369 Experiments 220 185 116 170 224 236 133 510 377 Database knowledge 3 24 19 970 31 33 2002 216 430 Text mining 1174 279 171 722 498 224 93 95 38 Shared domain 0 0 0 20915 0 42805 17792 6070 6478 Sequence similarity 8524 777 0 1345 48 921 77 9 244 Interologs 0 0 0 0 0 0 1701 1600 34 PDB 0 0 0 5082 0 0 864 4683 5487 Coexpression 6538 0 0 225 0 3559 4 12856 4523 Combined Score 6844 145 55 30142 1655 48848 29776 25904 18527

Table 1: Data source and confidence range (low confidence: scores less than 0.3; medium confidence: scores from 0.3 to 0.7; high confidence: scores greater than 0.7) of the functional networks for MLP, MTB and MSM.