Phylogenetic tree test ====================== Pairwise project comparison --------------------------- Bacteria ------------------------------------------------------------------------------------------------------------------ | Projects # trees Darwin LeastSquare Trees RaxML MaxLikelihood Trees | | Project Oma on ISet Project Oma on ISet | |----------------------------------------------------------------------------------------------------------------| | orthoMCL 390 0.448 +- 0.033 0.478 +- 0.033 0.448 +- 0.033 0.476 +- 0.034 | | BBH 9926 0.3508 +- 0.0063 0.3771 +- 0.0064 0.3638 +- 0.0064 0.3872 +- 0.0064 | | COG 4096 0.474 +- 0.011 0.552 +- 0.010 0.472 +- 0.011 0.546 +- 0.011 | | RoundUp 9962 0.4049 +- 0.0065 0.4173 +- 0.0064 0.4177 +- 0.0065 0.4270 +- 0.0065 | | eggNOG 9967 0.3253 +- 0.0067 0.4277 +- 0.0069 0.3323 +- 0.0068 0.4368 +- 0.0070 | | OMA Group 10112 0.4403 +- 0.0066 0.4285 +- 0.0065 0.4447 +- 0.0066 0.4376 +- 0.0066 | | RSD 10059 0.3417 +- 0.0062 0.3688 +- 0.0063 0.3580 +- 0.0064 0.3842 +- 0.0064 | ------------------------------------------------------------------------------------------------------------------ Eukaryota ------------------------------------------------------------------------------------------------------------------ | Projects # trees Darwin LeastSquare Trees RaxML MaxLikelihood Trees | | Project Oma on ISet Project Oma on ISet | |----------------------------------------------------------------------------------------------------------------| | ENSEMBL 4319 0.8433 +- 0.0078 0.8720 +- 0.0073 0.8455 +- 0.0078 0.8665 +- 0.0073 | | orthoMCL 1137 0.809 +- 0.019 0.9543 +- 0.0089 0.801 +- 0.019 0.926 +- 0.012 | | Homologene 802 0.944 +- 0.012 0.943 +- 0.012 0.917 +- 0.014 0.907 +- 0.014 | | Inparanoid 5945 0.9165 +- 0.0052 0.9290 +- 0.0047 0.8971 +- 0.0057 0.8971 +- 0.0057 | | eggNOG 2615 0.514 +- 0.016 0.9385 +- 0.0065 0.499 +- 0.016 0.9053 +- 0.0082 | | BBH 5675 0.8508 +- 0.0066 0.8807 +- 0.0060 0.8428 +- 0.0069 0.8638 +- 0.0065 | | RoundUp 1451 0.9418 +- 0.0089 0.9446 +- 0.0087 0.898 +- 0.011 0.905 +- 0.011 | | RSD 5737 0.8207 +- 0.0072 0.8747 +- 0.0061 0.8111 +- 0.0075 0.8553 +- 0.0067 | | OMA Group 3492 0.9063 +- 0.0068 0.8771 +- 0.0076 0.8860 +- 0.0076 0.8651 +- 0.0080 | ------------------------------------------------------------------------------------------------------------------ Fungi ------------------------------------------------------------------------------------------------------------------ | Projects # trees Darwin LeastSquare Trees RaxML MaxLikelihood Trees | | Project Oma on ISet Project Oma on ISet | |----------------------------------------------------------------------------------------------------------------| | RoundUp 1217 0.830 +- 0.015 0.835 +- 0.015 0.851 +- 0.015 0.849 +- 0.015 | | Inparanoid 3616 0.8476 +- 0.0078 0.8486 +- 0.0078 0.8771 +- 0.0075 0.8749 +- 0.0076 | | orthoMCL 3724 0.774 +- 0.010 0.8294 +- 0.0082 0.797 +- 0.010 0.8526 +- 0.0082 | | eggNOG 4239 0.483 +- 0.012 0.8313 +- 0.0075 0.502 +- 0.012 0.8636 +- 0.0072 | | BBH 3971 0.8152 +- 0.0081 0.8245 +- 0.0078 0.8564 +- 0.0076 0.8641 +- 0.0075 | | RSD 3873 0.8126 +- 0.0083 0.8299 +- 0.0080 0.8528 +- 0.0079 0.8603 +- 0.0078 | | OMA Group 2050 0.860 +- 0.010 0.853 +- 0.010 0.875 +- 0.010 0.870 +- 0.010 | ------------------------------------------------------------------------------------------------------------------ Comparison on Intersection sets ------------------------------- Bacteria ------------------------------------------------------------------- | Projects # trees RF dist | | LS Trees ML Trees | |-----------------------------------------------------------------| | BBH 1295 0.640 +- 0.019 0.608 +- 0.019 | | COG 1295 0.580 +- 0.019 0.562 +- 0.020 | | OMA 1295 0.644 +- 0.018 0.602 +- 0.019 | | OMA Group 1295 0.653 +- 0.018 0.617 +- 0.019 | | RSD 1295 0.636 +- 0.019 0.608 +- 0.019 | | RoundUp 1295 0.631 +- 0.019 0.605 +- 0.019 | ------------------------------------------------------------------- Eukaryota --------------------------------------------------------------- | Projects # trees RF dist | | LS Trees ML Trees | |-------------------------------------------------------------| | BBH 217 232 0.972 +- 0.016 0.940 +- 0.023 | | ENSEMBL 232 0.957 +- 0.020 0.957 +- 0.019 | | Inparanoid 232 0.968 +- 0.017 0.940 +- 0.024 | | OMA 232 0.972 +- 0.016 0.944 +- 0.023 | | RSD 217 232 0.966 +- 0.018 0.942 +- 0.022 | | eggNOG 232 0.582 +- 0.058 0.612 +- 0.056 | | orthoMCL 232 0.890 +- 0.036 0.869 +- 0.037 | --------------------------------------------------------------- Fungi ------------------------------------------------------------------- | Projects # trees RF dist | | LS Trees ML Trees | |-----------------------------------------------------------------| | BBH 1121 0.834 +- 0.015 0.854 +- 0.015 | | OMA 1121 0.836 +- 0.015 0.851 +- 0.015 | | RSD 1121 0.833 +- 0.015 0.853 +- 0.015 | | RoundUp 1121 0.834 +- 0.015 0.853 +- 0.015 | | eggNOG 1120 0.519 +- 0.024 0.536 +- 0.025 | | orthoMCL 1121 0.801 +- 0.017 0.824 +- 0.017 | ------------------------------------------------------------------- Literature ========== Pairwise project comparison --------------------------- --------------------------------------------------------------------------------------------- | Project | OMA | | FPR TPR | FPR TPR | |------------------------------------------------------|------------------------------------| | RoundUp 0.0905 +- 0.037 0.7525 +- 0.156 | 0.0733 +- 0.035 0.8077 +- 0.126 | | Inparanoid 0.0851 +- 0.050 0.6077 +- 0.172 | 0.0433 +- 0.043 0.8016 +- 0.153 | | ENSEMBL 0.1128 +- 0.068 0.7431 +- 0.225 | 0.0381 +- 0.041 0.8247 +- 0.187 | | orthoMCL 0.1200 +- 0.067 0.7428 +- 0.248 | 0.0577 +- 0.063 0.7406 +- 0.256 | | KOG 0.2275 +- 0.118 0.7047 +- 0.508 | 0.0464 +- 0.070 0.5468 +- 0.521 | | COG 0.8870 +- 0.033 0.9468 +- 0.121 | 0.1353 +- 0.039 0.8767 +- 0.124 | | Homologene 0.1139 +- 0.089 0.8333 +- 0.177 | 0.0611 +- 0.068 0.8481 +- 0.176 | | eggNOG 0.4986 +- 0.116 0.8482 +- 0.205 | 0.0664 +- 0.059 0.6668 +- 0.249 | | BBH 0.1060 +- 0.039 0.7998 +- 0.102 | 0.0692 +- 0.033 0.7928 +- 0.103 | | RSD 0.0901 +- 0.029 0.7545 +- 0.124 | 0.0692 +- 0.033 0.7928 +- 0.103 | | OMA Group 0.0334 +- 0.025 0.6328 +- 0.107 | 0.0692 +- 0.033 0.7928 +- 0.103 | --------------------------------------------------------------------------------------------- Comparison on Intersection set ------------------------------ --------------------------------------------------------- | Project FPR TPR | |-------------------------------------------------------| | OMA 0.0840 +- 0.053 0.8009 +- 0.167 | | RoundUp 0.0973 +- 0.057 0.5972 +- 0.169 | | Inparanoid 0.1391 +- 0.065 0.5602 +- 0.170 | | ENSEMBL 0.1874 +- 0.070 0.6713 +- 0.188 | | orthoMCL 0.1827 +- 0.069 0.8102 +- 0.166 | | Homologene 0.1373 +- 0.065 0.7824 +- 0.168 | | BBH 0.1373 +- 0.065 0.7917 +- 0.168 | | RSD 0.0840 +- 0.053 0.6944 +- 0.181 | | OMA Group 0.0688 +- 0.051 0.6065 +- 0.168 | --------------------------------------------------------- Gene Ontology Similarity ======================== Pairwise project comparison --------------------------- -------------------------------------------------------------------------------- | Project Result of Project | Result of OMA Pairwise | | Orthologs Similarity | Orthologs Similarity | |----------------------------------------------|-------------------------------| | COG 21309 0.4269 +- 0.0024 | 1377 0.547 +- 0.012 | | KOG 13779 0.5214 +- 0.0043 | 2877 0.5665 +- 0.0093 | | eggNOG 328772 0.42870 +- 0.00086 | 7556 0.5296 +- 0.0061 | | orthoMCL 12368 0.5233 +- 0.0047 | 7130 0.5319 +- 0.0063 | | Inparanoid 9306 0.5196 +- 0.0053 | 6853 0.5425 +- 0.0065 | | Homologene 4893 0.5509 +- 0.0073 | 5275 0.5444 +- 0.0071 | | ENSEMBL 8405 0.4971 +- 0.0060 | 5859 0.5061 +- 0.0073 | | RoundUp 5029 0.5536 +- 0.0073 | 5944 0.5494 +- 0.0069 | | OMA Pairwise 9885 0.5192 +- 0.0054 | n.a. n.a. | | OMA Group 5452 0.5227 +- 0.0073 | 9885 0.5192 +- 0.0054 | | RSD 9529 0.5281 +- 0.0054 | 9885 0.5192 +- 0.0054 | | BBH 10221 0.5274 +- 0.0052 | 9885 0.5192 +- 0.0054 | -------------------------------------------------------------------------------- Comparison on Intersection set ------------------------------ ------------------------------------------------ | Project Orthologs Similarity | |----------------------------------------------| | COG n.a. n.a. | | KOG n.a. n.a. | | eggNOG n.a. n.a. | | orthoMCL 3953 0.5391 +- 0.0088 | | Inparanoid 2932 0.5082 +- 0.0096 | | Homologene 2203 0.563 +- 0.012 | | ENSEMBL 3670 0.5378 +- 0.0091 | | RoundUp 2047 0.551 +- 0.012 | | OMA Pairwise 2390 0.553 +- 0.012 | | OMA Group 1323 0.567 +- 0.015 | | RSD 2331 0.554 +- 0.011 | | BBH 2533 0.554 +- 0.011 | ------------------------------------------------ EC number conservation ====================== Pairwise project comparison --------------------------- ------------------------------------------------------------------------------------- | Project Result of Project Result of OMA Pairwise | | Orthologs same EC class Orthologs same EC class | |-----------------------------------------------------------------------------------| | COG 210062 0.9163 +- 0.0012 125482 0.99148 +- 0.00051 | | KOG 7285 0.8524 +- 0.0081 2816 0.9606 +- 0.0072 | | eggNOG 1174585 0.76158 +- 0.00077 571500 0.99598 +- 0.00016 | | orthoMCL 42330 0.9284 +- 0.0025 27049 0.9768 +- 0.0018 | | Inparanoid 11363 0.9242 +- 0.0049 10442 0.9665 +- 0.0035 | | Homologene 4815 0.9782 +- 0.0041 6071 0.9699 +- 0.0043 | | ENSEMBL 5217 0.9323 +- 0.0068 4543 0.9694 +- 0.0050 | | RoundUp 1179563 0.99179 +- 0.00016 1108267 0.99546 +- 0.00013 | | OMA Pairwise 3392520 0.996881 +- 0.000059 n.a. n.a. | | OMA Group 2045541 0.998976 +- 0.000044 3392520 0.996881 +- 0.000059 | | RSD 3821815 0.993499 +- 0.000081 3392520 0.996881 +- 0.000059 | | BBH 3853220 0.993402 +- 0.000081 3392520 0.996881 +- 0.000059 | ------------------------------------------------------------------------------------- Comparison on Intersection set ------------------------------ ----------------------------------------------- | Project Orthologs EC cons. | |---------------------------------------------| | COG n.a. n.a. | | KOG n.a. n.a. | | eggNOG n.a. n.a. | | orthoMCL 2702 0.9297 +- 0.0096 | | Inparanoid 1841 0.934 +- 0.011 | | Homologene 1537 0.9779 +- 0.0074 | | ENSEMBL 2211 0.925 +- 0.011 | | RoundUp 1342 0.9784 +- 0.0078 | | OMA Pairwise 1839 0.9679 +- 0.0081 | | OMA Group 1036 0.9894 +- 0.0062 | | RSD 1485 0.9690 +- 0.0088 | | BBH 1613 0.9709 +- 0.0082 | ----------------------------------------------- Expression Correlation ====================== Pairwise project comparison --------------------------- ------------------------------------------------------------------------------- | Project Result of Project | Result of OMA Pairwise | | Orthologs mean correlation | Orthologs mean correlation | |----------------------------------------------|------------------------------| | COG n.a. n.a. | n.a. n.a. | | KOG n.a. n.a. | n.a. n.a. | | eggNOG 308106 0.01689 +- 0.00080 | 6592 0.2220 +- 0.0078 | | orthoMCL 7906 0.1832 +- 0.0070 | 5947 0.2206 +- 0.0082 | | Inparanoid 5701 0.2135 +- 0.0084 | 5572 0.2123 +- 0.0084 | | Homologene 3808 0.225 +- 0.010 | 3915 0.218 +- 0.010 | | ENSEMBL 7349 0.2172 +- 0.0074 | 8449 0.2140 +- 0.0068 | | RoundUp 3389 0.221 +- 0.011 | 4493 0.2202 +- 0.0095 | | OMA Pairwise 10919 0.2141 +- 0.0060 | n.a. n.a. | | OMA Group 9882 0.2148 +- 0.0063 | 10919 0.2141 +- 0.0060 | | RSD 10221 0.2141 +- 0.0062 | 10919 0.2141 +- 0.0060 | | BBH 10662 0.2119 +- 0.0061 | 10919 0.2141 +- 0.0060 | ------------------------------------------------------------------------------- Comparison on Intersection set ------------------------------ ---------------------------------------------- | Project Orthologs mean correlation | |--------------------------------------------| | COG n.a. n.a. | | KOG n.a. n.a. | | eggNOG n.a. n.a. | | orthoMCL 3085 0.186 +- 0.011 | | Inparanoid 2423 0.218 +- 0.013 | | Homologene 2357 0.220 +- 0.013 | | ENSEMBL 2196 0.222 +- 0.014 | | RoundUp 2140 0.218 +- 0.014 | | OMA Pairwise 2424 0.219 +- 0.013 | | OMA Group 2249 0.220 +- 0.013 | | RSD 2225 0.219 +- 0.013 | | BBH 2343 0.221 +- 0.013 | ---------------------------------------------- Gene Neighborhood conservation ============================== Pairwise project comparison --------------------------- ------------------------------------------------------------------------------------ | Project Result of Project | Result of OMA Pairwise | | Orthologs Cons. Gene Order | Orthologs Cons. Gene Order | |------------------------------------------------|---------------------------------| | COG 2344648 0.06156 +- 0.00031 | 264969 0.2801 +- 0.0017 | | KOG 153359 0.0522 +- 0.0011 | 14877 0.0196 +- 0.0022 | | eggNOG 55154352 0.045815 +- 0.000055 | 4212745 0.27549 +- 0.00043 | | orthoMCL 628080 0.07587 +- 0.00065 | 311608 0.1230 +- 0.0012 | | Inparanoid 1615850 0.27543 +- 0.00069 | 1195199 0.28965 +- 0.00081 | | Homologene 78887 0.2069 +- 0.0028 | 90333 0.1847 +- 0.0025 | | ENSEMBL 3170001 0.36125 +- 0.00053 | 2062315 0.43821 +- 0.00068 | | RoundUp 4782660 0.24437 +- 0.00039 | 4775526 0.25179 +- 0.00039 | | OMA Pairwise 39168985 0.22459 +- 0.00013 | n.a. n.a. | | OMA Group 19068944 0.32869 +- 0.00021 | 39168985 0.22459 +- 0.00013 | | RSD 48319491 0.21565 +- 0.00012 | 39168985 0.22459 +- 0.00013 | | BBH 48087906 0.21899 +- 0.00012 | 39168985 0.22459 +- 0.00013 | ------------------------------------------------------------------------------------ Comparison on Intersection set ------------------------------ ----------------------------------------------- | Project Orthologs Cons. Gene Order | |---------------------------------------------| | COG n.a. n.a. | | KOG n.a. n.a. | | eggNOG n.a. n.a. | | orthoMCL 15055 0.1479 +- 0.0057 | | Inparanoid 10103 0.1505 +- 0.0070 | | Homologene 9244 0.2098 +- 0.0083 | | ENSEMBL 14643 0.1395 +- 0.0056 | | RoundUp 8249 0.2108 +- 0.0088 | | OMA Pairwise 10102 0.2064 +- 0.0079 | | OMA Group 5795 0.313 +- 0.012 | | RSD 9528 0.1930 +- 0.0079 | | BBH 10016 0.1879 +- 0.0077 | -----------------------------------------------