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Analytical derivation of the prior XSwap probability of a hetnet edge
metaedge abbreviation n_edges n_connected_source_nodes n_connected_target_nodes n_source_wedges n_target_wedges n_wedges n_valid_xswaps
Anatomy–downregulates–Gene AdG 102240 36 15097 173440264 493897 173934161 5052523519
Anatomy–expresses–Gene AeG 526407 241 18094 2290279787 10749138 2301028925 136250872696
Anatomy–upregulates–Gene AuG 97848 36 15929 149352969 359661 149712630 4637353998
Compound–binds–Gene CbG 11571 1389 1689 104024 476540 580564 66357671
Compound–causes–Side Effect CcSE 138944 1071 5701 16998055 16764774 33762829 9618885267
Compound–downregulates–Gene CdG 21102 734 2880 1683615 291789 1975404 220661247
Compound–palliates–Disease CpD 390 221 50 326 2857 3183 72672
Compound–resembles–Compound CrC 12972 1281 1281 120047 120047 240094 83889812
Compound–treats–Disease CtD 755 387 77 1420 8070 9490 275145
Compound–upregulates–Gene CuG 18756 703 3247 1489248 183634 1672882 174211508
Disease–associates–Gene DaG 12623 134 5392 1581400 35550 1616950 78046803
Disease–downregulates–Gene DdG 7623 44 5745 884813 2498 887311 28163942
Disease–localizes–Anatomy DlA 3602 133 398 72644 19982 92626 6392775
Disease–presents–Symptom DpS 3357 133 415 64389 23430 87819 5545227
Disease–resembles–Disease DrD 1086 129 129 6531 6531 13062 576093
Disease–upregulates–Gene DuG 7731 44 5630 909467 3031 912498 28967817
Gene–covaries–Gene GcG 123380 12453 12453 3702610 3702610 7405220 7603845290
Gene–interacts–Gene GiG 294328 15165 15165 55412782 55412782 110825564 43203513064
Gene–participates–Biological Process GpBP 559504 14772 11381 30123408 90103196 120226604 156401856652
Gene–participates–Cellular Component GpCC 73566 10580 1391 456449 12531792 12988241 2692953154
Gene–participates–Molecular Function GpMF 97222 13063 2884 591373 15444939 16036312 4709973719
Gene–participates–Pathway GpPW 84372 8979 1822 1337526 11008146 12345672 3546929334
Gene→regulates→Gene Gr>G 265672 4634 7048 15056962 37821797 52878759 35237794197
Pharmacologic Class–includes–Compound PCiC 1029 345 724 3156 603 3759 525147
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@dhimmel dhimmel commented Sep 21, 2018

Here is the outputted estimated-xswap-priors.png:

estimated-xswap-priors

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@dhimmel dhimmel commented Sep 22, 2018

Here's a plot that uses ggplot2::geom_linerange to draw rough confidence intervals:

estimated-xswap-priors

The CIs are very tight.

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@dhimmel dhimmel commented Sep 24, 2018

Updated figure from this notebook that includes two metaedges:

xswap-versus-analytic-priors

Includes Disease-associates-Gene data from greenelab/snorkeling#67.

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