Spreadsheet: 6757b0e1-2442-4028-afc6-bfbc8c8604da
Sheet: Sheet1

Table S2.  Sensitivity, specificity, and predicted accuracy of eight gene association methods | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6 | Unnamed: 7 | Unnamed: 8 | Unnamed: 9 | Unnamed: 10 | Unnamed: 11 | Unnamed: 12 | Unnamed: 13 | Unnamed: 14 | Unnamed: 15 | Unnamed: 16 | Unnamed: 17 | Unnamed: 18 | Unnamed: 19 | Unnamed: 20 | Unnamed: 21 | Unnamed: 22 | Unnamed: 23 | Unnamed: 24
1.  Top 100 genes compared to genes in Slice 1 (top101~1000), [NAME] (mid 1-900)  and [NAME] (bottom 1-900) from sorted gene list with most coexpressed gene located at the top.  The numbers of positive genes from thhree slices containing 900 genes were divided by 9 before they were compared to top 100
Same pathway ( genes in the same pathway are counted as positives) | TP_top1-100 | FP_top1~100 | TN_top101~900 (Avg/100) | FN_top101-1000 (Avg/100) | Sensitivity=(TP/TP+FN)x100% | Specificity (TN/(FP+TN)*100% | Predicted accuracy (TP+TN)/(TP+FP+TN+FN)*100 |  | TP_top1-100 | FP_top1~100 | TN-mid1~900( avg/100) | FN-mid1-900 (Avg/100) | Sensitivity=(TP/TP+FN)x100% | Specificity (TN/(FP+TN)*100% | Predicted accuracy (TP+TN)/(TP+FP+TN+FN)*100 |  | TP_top1-100 | FP_top1~100 | TN-bottom1~900(Avg/100) | FN-bottom1~900 (Avg per 100) | Sensitivity=(TP/TP+FN)x100% | Specificity (TN/(FP+TN)*100% | Predicted accuracy (TP+TN)/(TP+FP+TN+FN)*100
dist.corr | 8 | 92 | 93.3 | 6.7 | 54.421768707483 | 50.35078251484079 | 50.64999999999999 |  | 8 | 92 | 99.9 | 0.1 | 98.76543209876544 | 52.05836373110996 | 53.95 |  | 8 | 92 | 100 | 0 | 100 | 52.08333333333334 | 54
[NAME] | 18 | 82 | 91.3 | 8.7 | 67.41573033707866 | 52.68320830929024 | 54.65 |  | 18 | 82 | 100 | 0 | 100 | 54.94505494505495 | 59 |  | 18 | 82 | 100 | 0 | 100 | 54.94505494505495 | 59
kendall | 16 | 84 | 89.9 | 10.1 | 61.30268199233716 | 51.69637722829212 | 52.95000000000001 |  | 16 | 84 | 100 | 0 | 100 | 54.34782608695652 | 57.99999999999999 |  | 16 | 84 | 100 | 0 | 100 | 54.34782608695652 | 57.99999999999999
pearson | 6 | 94 | 96.9 | 3.1 | 65.93406593406593 | 50.75955997904662 | 51.45000000000001 |  | 6 | 94 | 99.8 | 0.2 | 96.77419354838709 | 51.49638802889577 | 52.90000000000001 |  | 6 | 94 | 100 | 0 | 100 | 51.54639175257731 | 53
rank.theil | 6 | 94 | 95.3 | 4.7 | 56.07476635514019 | 50.34337031167458 | 50.64999999999999 |  | 6 | 94 | 99.9 | 0.1 | 98.36065573770493 | 51.5214027849407 | 52.95000000000001 |  | 6 | 94 | 100 | 0 | 100 | 51.54639175257731 | 53
spearman | 15 | 85 | 90.8 | 9.2 | 61.98347107438017 | 51.64960182025028 | 52.90000000000001 |  | 15 | 85 | 100 | 0 | 100 | 54.05405405405406 | 57.49999999999999 |  | 15 | 85 | 100 | 0 | 100 | 54.05405405405406 | 57.49999999999999
theil.sen | 2 | 98 | 97.6 | 2.4 | 45.45454545454545 | 49.89775051124744 | 49.8 |  | 2 | 98 | 99.9 | 0.1 | 95.23809523809523 | 50.4800404244568 | 50.95 |  | 2 | 98 | 100 | 0 | 100 | 50.50505050505051 | 51
wt.rank.corr | 12 | 88 | 91.8 | 8.2 | 59.4059405940594 | 51.05672969966629 | 51.9 |  | 12 | 88 | 100 | 0 | 100 | 53.19148936170212 | 56.00000000000001 |  | 12 | 88 | 100 | 0 | 100 | 53.19148936170212 | 56.00000000000001
different pathways ( ( genes in the different pathway are counted as positives) | TP_top1-100 | FP_top1~100 | TN_top101~900 (Avg/100) | FN_top101-1000 (Avg/100) | Sensitivity=(TP/TP+FN)x100% | Specificity (TN/(FP+TN)*100% | Predicted accuracy (TP+TN)/(TP+FP+TN+FN)*100 |  | TP_top1-100 | FP_top1~100 | TN-mid1~900( avg/100) | FN-mid1-900 (Avg/100) | Sensitivity=(TP/TP+FN)x100% | Specificity (TN/(FP+TN)*100% | Predicted accuracy (TP+TN)/(TP+FP+TN+FN)*100 |  | TP_top1-100 | FP_top1~100 | TN-bottom1~900(Avg/100) | FN-bottom1~900 (Avg per 100) | Sensitivity=(TP/TP+FN)x100% | Specificity (TN/(FP+TN)*100% | Predicted accuracy (TP+TN)/(TP+FP+TN+FN)*100
dist.corr | 0 | 100 | 94.9 | 5.1 | 0 | 48.6916367367881 | 47.45 |  | 0 | 100 | 98.2 | 1.8 | 0 | 49.54591321897074 | 49.1 |  | 0 | 100 | 98.3 | 1.7 | 0 | 49.57135653050933 | 49.15
[NAME] | 4 | 96 | 95.6 | 4.4 | 47.61904761904761 | 49.89561586638831 | 49.8 |  | 4 | 96 | 98.2 | 1.8 | 68.96551724137932 | 50.56642636457261 | 51.1 |  | 4 | 96 | 99.2 | 0.8 | 83.33333333333334 | 50.81967213114754 | 51.6
kendall | 6 | 94 | 94.7 | 5.3 | 53.09734513274336 | 50.18547959724431 | 50.35000000000001 |  | 6 | 94 | 97.8 | 2.2 | 73.17073170731709 | 50.99061522419186 | 51.9 |  | 6 | 94 | 98.2 | 1.8 | 76.92307692307693 | 51.09261186264309 | 52.1
pearson | 2 | 98 | 97.6 | 2.4 | 45.45454545454545 | 49.89775051124744 | 49.8 |  | 2 | 98 | 97.7 | 2.3 | 46.51162790697674 | 49.92335206949413 | 49.85 |  | 2 | 98 | 98.2 | 1.8 | 52.63157894736842 | 50.05096839959226 | 50.1
rank.theil | 5 | 95 | 95.9 | 4.1 | 54.94505494505495 | 50.2357255107386 | 50.45 |  | 5 | 95 | 98.9 | 1.1 | 81.9672131147541 | 51.00567302733368 | 51.95000000000001 |  | 5 | 95 | 97.3 | 2.7 | 64.93506493506493 | 50.59802392095683 | 51.15
spearman | 6 | 94 | 95.1 | 4.9 | 55.04587155963303 | 50.29085140137494 | 50.55 |  | 6 | 94 | 97.6 | 2.4 | 71.42857142857143 | 50.93945720250522 | 51.8 |  | 6 | 94 | 98.2 | 1.8 | 76.92307692307693 | 51.09261186264309 | 52.1
theil.sen | 4 | 96 | 96.3 | 3.7 | 51.94805194805194 | 50.07800312012481 | 50.14999999999999 |  | 4 | 96 | 98.4 | 1.6 | 71.42857142857143 | 50.61728395061728 | 51.2 |  | 4 | 96 | 98.4 | 1.6 | 71.42857142857143 | 50.61728395061728 | 51.2
wt.rank.corr | 4 | 96 | 95.1 | 4.9 | 44.9438202247191 | 49.76452119309262 | 49.55 |  | 4 | 96 | 97.6 | 2.4 | 62.5 | 50.41322314049587 | 50.8 |  | 4 | 96 | 98.6 | 1.4 | 74.07407407407408 | 50.66803699897225 | 51.3
2.  Top 500 genes compared to genes in Slice 1 (top501~1000), [NAME] (mid 1-500)  and [NAME] (bottom 1-500) from sorted gene list with most coexpressed gene located.  Top 500 genes can compare to other slices directly because they have the same numbers of genes
Same pathway ( genes in the same pathway are counted as positives) | TP_top1-500 | FP_top1-500 | TN501~1000 (Average) | FN501~1000 (Average) | Sensitivity=(TP/TP+FN)x100% | Specificity (TN/(FP+TN)*100% | Predicted accuracy (TP+TN)/(TP+FP+TN+FN)*100 |  | TP_top1-500 | FP_top1-500 | TN-mid1-500 | FN_mid1~500 | Sensitivity=(TP/TP+FN)x100% | Specificity (TN/(FP+TN)*100% | Predicted accuracy (TP+TN)/(TP+FP+TN+FN)*100 |  | TP_top1-500 | FP_top1-500 | TN-bottom1-500 | FN_bottom1-500 | Sensitivity=(TP/TP+FN)x100% | Specificity (TN/(FP+TN)*100% | Predicted accuracy (TP+TN)/(TP+FP+TN+FN)*100
dist.corr | 50 | 450 | 482 | 18 | 73.52941176470588 | 51.7167381974249 | 53.2 |  | 50 | 450 | 499 | 1 | 98.0392156862745 | 52.58166491043204 | 54.90000000000001 |  | 50 | 450 | 500 | 0 | 100 | 52.63157894736842 | 55.00000000000001
[NAME] | 65 | 435 | 469 | 31 | 67.70833333333334 | 51.88053097345132 | 53.40000000000001 |  | 65 | 435 | 500 | 0 | 100 | 53.47593582887701 | 56.49999999999999 |  | 65 | 435 | 500 | 0 | 100 | 53.47593582887701 | 56.49999999999999
kendall | 62 | 438 | 455 | 45 | 57.94392523364485 | 50.9518477043673 | 51.7 |  | 62 | 438 | 500 | 0 | 100 | 53.30490405117271 | 56.2 |  | 62 | 438 | 500 | 0 | 100 | 53.30490405117271 | 56.2
pearson | 30 | 470 | 496 | 4 | 88.23529411764706 | 51.34575569358179 | 52.6 |  | 30 | 470 | 498 | 2 | 93.75 | 51.44628099173553 | 52.8 |  | 30 | 470 | 500 | 0 | 100 | 51.54639175257731 | 53
rank.theil | 30 | 470 | 482 | 18 | 62.5 | 50.63025210084034 | 51.2 |  | 30 | 470 | 499 | 1 | 96.7741935483871 | 51.49638802889577 | 52.90000000000001 |  | 30 | 470 | 500 | 0 | 100 | 51.54639175257731 | 53
spearman | 64 | 436 | 466 | 34 | 65.3061224489796 | 51.66297117516629 | 53 |  | 64 | 436 | 500 | 0 | 100 | 53.41880341880342 | 56.39999999999999 |  | 64 | 436 | 500 | 0 | 100 | 53.41880341880342 | 56.39999999999999
theil.sen | 11 | 489 | 487 | 13 | 45.83333333333333 | 49.89754098360656 | 49.8 |  | 11 | 489 | 500 | 0 | 100 | 50.55611729019211 | 51.1 |  | 11 | 489 | 499 | 1 | 91.66666666666666 | 50.50607287449392 | 51
wt.rank.corr | 52 | 448 | 466 | 34 | 60.46511627906976 | 50.98468271334792 | 51.8 |  | 52 | 448 | 500 | 0 | 100 | 52.74261603375528 | 55.2 |  | 52 | 448 | 500 | 0 | 100 | 52.74261603375528 | 55.2
different pathways ( ( genes in the different pathway are counted as positives) | TP_top1-500 | FP_top1-500 | TN501~1000 (Average) | FN501~1000 (Average) | Sensitivity=(TP/TP+FN)x100% | Specificity (TN/(FP+TN)*100% | Predicted accuracy (TP+TN)/(TP+FP+TN+FN)*100 |  | TP_top1-500 | FP_top1-500 | TN-mid1-500 | FN_mid1-500 | Sensitivity=(TP/TP+FN)x100% | Specificity (TN/(FP+TN)*100% | Predicted accuracy (TP+TN)/(TP+FP+TN+FN)*100 |  | TP_top1-500 | FP_top1-500 | TN-bottom1-500 | FN_bottom1-500 | Sensitivity=(TP/TP+FN)x100% | Specificity (TN/(FP+TN)*100% | Predicted accuracy (TP+TN)/(TP+FP+TN+FN)*100
dist.corr | 20 | 480 | 474 | 26 | 43.47826086956522 | 49.68553459119497 | 49.4 |  | 20 | 480 | 493 | 7 | 74.07407407407408 | 50.66803699897225 | 51.3 |  | 20 | 480 | 491 | 9 | 68.96551724137932 | 50.56642636457261 | 51.1
[NAME] | 26 | 474 | 482 | 18 | 59.09090909090909 | 50.418410041841 | 50.8 |  | 26 | 474 | 490 | 10 | 72.22222222222221 | 50.8298755186722 | 51.6 |  | 26 | 474 | 497 | 3 | 89.65517241379311 | 51.18434603501545 | 52.3
kendall | 26 | 474 | 472 | 28 | 48.14814814814815 | 49.89429175475687 | 49.8 |  | 26 | 474 | 490 | 10 | 72.22222222222221 | 50.8298755186722 | 51.6 |  | 26 | 474 | 490 | 10 | 72.22222222222221 | 50.8298755186722 | 51.6
pearson | 14 | 486 | 490 | 10 | 58.33333333333334 | 50.20491803278689 | 50.4 |  | 14 | 486 | 489 | 11 | 56.00000000000001 | 50.15384615384615 | 50.3 |  | 14 | 486 | 492 | 8 | 63.63636363636363 | 50.30674846625767 | 50.6
rank.theil | 20 | 480 | 478 | 22 | 47.61904761904761 | 49.89561586638831 | 49.8 |  | 20 | 480 | 492 | 8 | 71.42857142857143 | 50.61728395061728 | 51.2 |  | 20 | 480 | 487 | 13 | 60.60606060606061 | 50.36194415718717 | 50.7
spearman | 22 | 478 | 472 | 28 | 44 | 49.68421052631579 | 49.4 |  | 22 | 478 | 486 | 14 | 61.11111111111111 | 50.4149377593361 | 50.8 |  | 22 | 478 | 486 | 14 | 61.11111111111111 | 50.4149377593361 | 50.8
theil.sen | 20 | 480 | 483 | 17 | 54.05405405405406 | 50.15576323987538 | 50.3 |  | 20 | 480 | 492 | 8 | 71.42857142857143 | 50.61728395061728 | 51.2 |  | 20 | 480 | 496 | 4 | 83.33333333333334 | 50.81967213114754 | 51.6
wt.rank.corr | 24 | 476 | 476 | 24 | 50 | 50 | 50 |  | 24 | 476 | 492 | 8 | 75 | 50.82644628099173 | 51.6 |  | 24 | 476 | 490 | 10 | 70.58823529411765 | 50.72463768115942 | 51.4
Note :   TP---True Positive          TN--- True Negative            FP---- False Positive           FN-----false negative
top---top genes of sorted list, mid---middle slice of sorted gene list,  bottom---bottom slice of sorted list