Comparison of multifunctional and other annotated genes for different organisms, as detected for Biological Process ontology using different co-annotation p-value thresholds (see Materials and Methods; the results presented in the main text are for p-value threshold 0.1). For each organism and for each co-annotation p-value threshold, the results of comparison with respect to several gene features are shown (for description of the features see the main text). In the first part, for each gene feature (e.g., protein sequence length), the number of genes with a defined value is shown for multifunctional genes (size), then mean +- standard deviation and median (med) of the feature for multifunctional genes, then the same statistics for other annotated genes, and finally the Mann-Whitney U test p-value. In the second part, for each set of genes of interest (e.g., essential genes curated by FlyBase), the number of multifunctional genes is shown (size) that belong to the set of interest or to the background (e.g., all genes with phenotype reported in FlyBase), fraction of multifunctional genes that belong to the set of interest, and p-value from hypergeometic test for significance of this intersection, then the number of other annotated genes (size) that belong to the set of interest or to the background, fraction of other annotated genes the belong to the set of interest, and p-value from hypergeometic test for significance of this intersection (if p-value for multifunctional genes is above 0.05). D. melanogaster =============== Compare groups multifunctional and other annotated genes for co-annotation p-value threshold 0.05 ------------------------------------------------------------------------------------------------------ length: size 1590 950.922 +- 1368.726 med 644.500 and size 4088 657.462 +- 656.422 med 478.500 MWU p-val 1.9e-42 domains: size 1569 2.349 +- 1.926 med 2.000 and size 3980 1.989 +- 1.545 med 2.000 MWU p-val 1.3e-09 disorder: size 1590 0.288 +- 0.255 med 0.231 and size 4088 0.230 +- 0.250 med 0.130 MWU p-val 1.2e-21 number of conditions where expressed (FlyAtlas): size 1542 25.453 +- 11.560 med 33.000 and size 3982 20.910 +- 13.446 med 27.000 MWU p-val 4.4e-30 number of conditions where expressed (modENCODE): size 1586 103.455 +- 26.024 med 118.000 and size 4128 86.961 +- 39.397 med 113.000 MWU p-val 8.0e-43 evolutionary conservation: size 1608 0.676 +- 0.153 med 0.702 and size 4215 0.632 +- 0.187 med 0.669 MWU p-val 1.5e-13 number of regulators: size 1555 19.241 +- 10.253 med 19.000 and size 3831 14.250 +- 9.804 med 14.000 MWU p-val 1.4e-57 number of genetic interactions: size 830 9.406 +- 15.900 med 4.000 and size 715 3.964 +- 5.612 med 2.000 MWU p-val 1.3e-28 degree: size 1181 13.899 +- 19.369 med 6.000 and size 2519 9.790 +- 14.076 med 4.000 MWU p-val 1.5e-16 betweenness: size 1181 22987.196 +- 58326.344 med 4124.432 and size 2519 11494.842 +- 27770.453 med 1143.509 MWU p-val 2.6e-21 participation: size 1181 0.574 +- 0.313 med 0.667 and size 2519 0.480 +- 0.340 med 0.500 MWU p-val 4.9e-15 essentiality (FlyBase curated): size 1575 fraction 0.735 hypergeom p-value 1.2e-94 and size 3710 fraction 0.430 essentiality (cell lines RNAi): size 1585 fraction 0.037 hypergeom p-value 6.2e-02 and size 4098 fraction 0.029 hypergeom p-value 9.6e-01 Compare groups multifunctional and other annotated genes for co-annotation p-value threshold 0.2 ----------------------------------------------------------------------------------------------------- length: size 1236 938.993 +- 1266.631 med 642.000 and size 4442 684.168 +- 792.953 med 489.000 MWU p-val 8.2e-32 domains: size 1223 2.352 +- 1.983 med 2.000 and size 4326 2.018 +- 1.562 med 2.000 MWU p-val 6.3e-06 disorder: size 1236 0.283 +- 0.252 med 0.223 and size 4442 0.236 +- 0.252 med 0.138 MWU p-val 6.3e-14 number of conditions where expressed (FlyAtlas): size 1198 25.543 +- 11.507 med 33.000 and size 4326 21.246 +- 13.367 med 28.000 MWU p-val 2.2e-23 number of conditions where expressed (modENCODE): size 1233 103.957 +- 25.497 med 118.000 and size 4481 88.123 +- 38.809 med 114.000 MWU p-val 2.2e-34 evolutionary conservation: size 1247 0.678 +- 0.157 med 0.705 and size 4576 0.634 +- 0.184 med 0.670 MWU p-val 7.2e-13 number of regulators: size 1209 19.428 +- 10.256 med 19.000 and size 4177 14.609 +- 9.911 med 15.000 MWU p-val 8.7e-46 number of genetic interactions: size 672 9.707 +- 16.129 med 4.000 and size 873 4.717 +- 8.252 med 2.000 MWU p-val 3.9e-20 degree: size 933 13.866 +- 18.903 med 6.000 and size 2767 10.169 +- 14.882 med 4.000 MWU p-val 1.3e-13 betweenness: size 933 22415.074 +- 52198.189 med 4124.432 and size 2767 12717.788 +- 35355.829 med 1257.672 MWU p-val 6.7e-17 participation: size 933 0.577 +- 0.309 med 0.667 and size 2767 0.488 +- 0.340 med 0.500 MWU p-val 9.6e-12 essentiality (FlyBase curated): size 1227 fraction 0.747 hypergeom p-value 1.4e-75 and size 4058 fraction 0.453 essentiality (cell lines RNAi): size 1232 fraction 0.039 hypergeom p-value 4.8e-02 and size 4451 fraction 0.029 H. sapiens ========== Compare groups multifunctional and other annotated genes for co-annotation p-value threshold 0.05 ------------------------------------------------------------------------------------------------------ length: size 2742 683.722 +- 918.503 med 483.000 and size 6838 600.477 +- 587.879 med 454.000 MWU p-val 1.5e-08 domains: size 2724 2.348 +- 1.782 med 2.000 and size 6776 2.084 +- 1.495 med 2.000 MWU p-val 1.0e-10 disorder: size 2742 0.222 +- 0.230 med 0.140 and size 6838 0.211 +- 0.230 med 0.121 MWU p-val 3.7e-04 number of organism parts where expressed (GNF Atlas): size 2421 6.821 +- 4.727 med 6.000 and size 5697 6.349 +- 4.338 med 5.000 MWU p-val 1.3e-04 number of organism parts where expressed (eGenetics): size 2263 32.015 +- 16.715 med 34.000 and size 5398 29.600 +- 17.043 med 31.000 MWU p-val 7.1e-09 evolutionary conservation: size 2718 0.544 +- 0.173 med 0.559 and size 6766 0.520 +- 0.181 med 0.539 MWU p-val 1.2e-08 number of regulators: size 2633 31.516 +- 19.250 med 32.000 and size 6375 29.909 +- 18.911 med 31.000 MWU p-val 3.2e-04 degree: size 2354 23.821 +- 32.892 med 11.000 and size 5082 15.691 +- 23.519 med 7.000 MWU p-val 1.3e-35 betweenness: size 2354 35136.951 +- 84899.009 med 5316.406 and size 5082 15059.621 +- 45006.435 med 1597.058 MWU p-val 2.2e-49 participation: size 2354 0.651 +- 0.284 med 0.750 and size 5082 0.571 +- 0.315 med 0.667 MWU p-val 7.6e-31 essentiality (mouse orthologs): size 1962 fraction 0.524 hypergeom p-value 1.0e-14 and size 3313 fraction 0.415 essentiality (cell lines RNAi): size 2683 fraction 0.204 hypergeom p-value 3.6e-36 and size 6713 fraction 0.104 with disease: size 2756 fraction 0.317 hypergeom p-value 5.3e-30 and size 6908 fraction 0.206 with two diseases: size 485 fraction 0.179 hypergeom p-value 2.7e-08 and size 663 fraction 0.072 Compare groups multifunctional and other annotated genes for co-annotation p-value threshold 0.2 ----------------------------------------------------------------------------------------------------- length: size 2183 690.696 +- 966.741 med 485.000 and size 7397 604.710 +- 597.118 med 455.000 MWU p-val 2.8e-08 domains: size 2170 2.343 +- 1.810 med 2.000 and size 7330 2.105 +- 1.511 med 2.000 MWU p-val 3.3e-07 disorder: size 2183 0.224 +- 0.228 med 0.146 and size 7397 0.211 +- 0.231 med 0.121 MWU p-val 8.5e-05 number of organism parts where expressed (GNF Atlas): size 1930 6.829 +- 4.773 med 6.000 and size 6188 6.384 +- 4.356 med 5.000 MWU p-val 1.8e-03 number of organism parts where expressed (eGenetics): size 1807 32.574 +- 16.680 med 35.000 and size 5854 29.616 +- 17.014 med 31.000 MWU p-val 5.5e-11 evolutionary conservation: size 2166 0.546 +- 0.174 med 0.563 and size 7318 0.521 +- 0.181 med 0.539 MWU p-val 1.1e-08 number of regulators: size 2094 31.912 +- 19.190 med 32.500 and size 6914 29.914 +- 18.950 med 31.000 MWU p-val 3.5e-05 degree: size 1880 24.822 +- 33.834 med 11.000 and size 5556 16.046 +- 24.013 med 7.000 MWU p-val 8.6e-35 betweenness: size 1880 37603.340 +- 89568.047 med 5815.683 and size 5556 15937.923 +- 46798.575 med 1710.893 MWU p-val 1.0e-46 participation: size 1880 0.659 +- 0.280 med 0.750 and size 5556 0.575 +- 0.314 med 0.667 MWU p-val 3.1e-29 essentiality (mouse orthologs): size 1588 fraction 0.543 hypergeom p-value 4.6e-17 and size 3687 fraction 0.418 essentiality (cell lines RNAi): size 2137 fraction 0.213 hypergeom p-value 4.0e-33 and size 7259 fraction 0.108 with disease: size 2191 fraction 0.328 hypergeom p-value 4.4e-28 and size 7473 fraction 0.212 with two diseases: size 403 fraction 0.196 hypergeom p-value 2.8e-09 and size 745 fraction 0.075 S. cerevisiae ============= Compare groups multifunctional and other annotated genes for co-annotation p-value threshold 0.05 ------------------------------------------------------------------------------------------------------ length: size 931 600.948 +- 413.615 med 502.000 and size 3627 516.752 +- 388.938 med 431.000 MWU p-val 1.0e-12 domains: size 912 2.060 +- 1.338 med 2.000 and size 3515 1.877 +- 1.270 med 1.000 MWU p-val 2.3e-05 disorder: size 931 0.238 +- 0.234 med 0.166 and size 3627 0.181 +- 0.217 med 0.090 MWU p-val 2.9e-15 evolutionary conservation: size 932 0.767 +- 0.159 med 0.786 and size 3622 0.750 +- 0.176 med 0.762 MWU p-val 1.6e-02 number of regulators: size 932 68.323 +- 28.291 med 65.000 and size 3602 65.361 +- 29.416 med 61.000 MWU p-val 1.1e-03 number of genetic interactions: size 928 98.502 +- 117.831 med 53.000 and size 3495 50.783 +- 75.126 med 24.000 MWU p-val 1.9e-60 degree: size 889 28.933 +- 30.319 med 20.000 and size 3371 20.994 +- 26.339 med 11.000 MWU p-val 5.9e-25 betweenness: size 889 11224.868 +- 23046.501 med 3476.411 and size 3371 6234.079 +- 16951.358 med 1145.588 MWU p-val 9.4e-30 participation: size 889 0.710 +- 0.233 med 0.790 and size 3371 0.600 +- 0.276 med 0.667 MWU p-val 1.9e-34 essentiality condition count (homozygous): size 714 33.444 +- 29.011 med 24.000 and size 2546 28.435 +- 25.439 med 22.000 MWU p-val 1.8e-04 essentiality condition count (heterozygous): size 797 31.880 +- 26.124 med 26.000 and size 3074 28.384 +- 21.976 med 24.000 MWU p-val 1.6e-03 essentiality: size 933 fraction 0.234 hypergeom p-value 9.5e-01 and size 3512 fraction 0.260 hypergeom p-value 5.4e-02 Compare groups multifunctional and other annotated genes for co-annotation p-value threshold 0.2 ----------------------------------------------------------------------------------------------------- length: size 788 593.421 +- 400.015 med 495.000 and size 3770 521.519 +- 393.492 med 435.000 MWU p-val 1.2e-09 domains: size 771 2.014 +- 1.296 med 2.000 and size 3656 1.893 +- 1.283 med 1.000 MWU p-val 4.3e-03 disorder: size 788 0.240 +- 0.236 med 0.164 and size 3770 0.183 +- 0.217 med 0.091 MWU p-val 1.2e-12 evolutionary conservation: size 789 0.770 +- 0.157 med 0.788 and size 3765 0.750 +- 0.176 med 0.763 MWU p-val 8.0e-03 number of regulators: size 789 68.726 +- 28.219 med 66.000 and size 3745 65.389 +- 29.385 med 61.000 MWU p-val 6.8e-04 number of genetic interactions: size 786 98.810 +- 119.634 med 54.000 and size 3637 52.579 +- 77.152 med 25.000 MWU p-val 4.7e-51 degree: size 748 28.027 +- 29.268 med 19.000 and size 3512 21.506 +- 26.857 med 11.000 MWU p-val 2.2e-17 betweenness: size 748 10845.138 +- 22534.751 med 3372.978 and size 3512 6515.326 +- 17429.915 med 1237.806 MWU p-val 4.7e-22 participation: size 748 0.708 +- 0.234 med 0.785 and size 3512 0.605 +- 0.275 med 0.667 MWU p-val 1.1e-27 essentiality condition count (homozygous): size 610 33.364 +- 29.046 med 24.000 and size 2650 28.650 +- 25.602 med 22.000 MWU p-val 7.6e-04 essentiality condition count (heterozygous): size 670 31.796 +- 26.561 med 26.000 and size 3201 28.540 +- 22.059 med 24.000 MWU p-val 1.1e-02 essentiality: size 790 fraction 0.235 hypergeom p-value 9.2e-01 and size 3655 fraction 0.259 hypergeom p-value 9.5e-02