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Table S0.

Comparison of LeMeDISCO’s  J-score with the XD score, NG, SAB score and symptom similarity for correlations with comorbidity quantified by the log(RR) score, φ–score and recalla.

Unbinnedb
10 binsb
Recall
Log(RR) scoreφ-scoreLog(RR) scoreφ-score
198,149 pairsc
LeMeDISCO0.312(0.0)0.218(0.0)0.933(8.1 x 10-5)0.900(3.9 x 10-4)49.7%
29,783 pairsd
LeMeDISCO0.185(0.0)0.138(0.0)0.939(5.6 x 10-5)0.829(3.0 x 10-3)56.0%
XD score260.050(5.9 x 10-18)0.082(0.0)0.445(0.20)0.252(0.48)6.5%
NGe0.008(0.17)0.058(1.3 x 10-23)-0.436-0.175-
947 pairsf
LeMeDISCO0.217(1.5 x10-11)0.282(9.0 x10-19)0.682(0.030)0.688(0.028)75.8%
SAB score28-0.188(5.5 x10-9)-0.218(1.2 x10-11)-0.671(0.034)-0.473(0.17)8.5%
2,630 pairsg
LeMeDISCO0.184(1.9x10-21)0.196(3.5x10-24)0.774(8.6 x10-3)0.654(0.040)71.1%
Symptom similarity270.337(0.0)0.197(1.6 x10-24)0.950(2.6 x10-5)0.960(1.1 x10-5)100%

a Numbers in parenthesis are the p-values of the corresponding correlation. Bold indicates the best results for the given data set.

b Unbinned means raw data; each pair is a data point. 10 bins: partitioning the prediction scores into 10 equal size bins. In each bin, the Log(RR) & φ–score are averaged over data points in the bin. This gives equal weight to the rare prediction scores in the correlation analysis.

c Mapping the DOID IDs from the human DO database to ICD9 IDs of Ref.25, gives a set of 198,149 disease pairs

d Mapped the ICD9 disease code to our DOID of DO and obtained a consensus subset of 29,783 pairs from Table S0 dataset of 97,665 pairs in Ref.26.

e NG is the number of shared genes between disease pairs in Ref.26.

f Consensus set of 947 disease pairs from the dataset of Ref.28 and our dataset of 198,149.

g A consensus dataset of 2,630 disease pairs was obtained from their Supplementary dataset 4 of Ref.27 compared to our set of 198,149 pairs.

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