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Subsections

Classification of specific FunCat trees

In this section we reported some example results achieved with TPR-w ensembles, relative to trees rooted at the highest level of the FunCat hierarchy. Considering the large amount of data, we reported results for only a subset of the highest level trees. Full data are available upon request from the author.

FunCat ID 01: Metabolism

Fig. 2 represents the FunCat tree rooted at the functional class "Metabolism".
Figure 2: Tree of the FunCat classes rooted at Funcat ID=01 (Metabolism).
\includegraphics[width = 18cm]{eps/tree.01.eps}

Tab. 2 shows the results obtained by TPR-w ensembles with the Pfam-1 data set.



Table 2: Classification results on the FunCat tree rooted at "Metabolism", using Pfam-1 data. Each row represents a functional class of the FunCat taxonomy. Prec. stands for precision, Rec. recall, Sp. specificity, F F-measure, Acc. accuracy.
FunCat ID Description Prec. Rec. Sp. F Acc.
01 Metabolism 0.8296 0.5880 0.9309 0.6882 0.8061
01.01 amino acid metabolism 0.6209 0.3392 0.9857 0.4387 0.9441
01.01.03 assimilation of ammonia, metabolism of the glutamate group 0.2692 0.1521 0.9945 0.1944 0.9835
01.01.03.02 metabolism of glutamate 0.3684 0.3181 0.9965 0.3414 0.9923
01.01.03.05 metabolism of arginine 0.0000 0.0000 0.9982 0.0000 0.9923
01.01.06 metabolism of the aspartate family 0.3823 0.2166 0.9939 0.2765 0.9807
01.01.06.05 metabolism of methionine 0.5294 0.2903 0.9977 0.3750 0.9914
01.01.09 metabolism of the cysteine - aromatic group 0.4878 0.2597 0.9939 0.3389 0.9778
01.01.13 regulation of amino acid metabolism 0.1000 0.0322 0.9974 0.0487 0.9889
01.02 nitrogen, sulfur and selenium metabolism 0.5483 0.2000 0.9959 0.2931 0.9767
01.02.07 regulation of nitrogen, sulfur and selenium metabolism 0.2727 0.1111 0.9977 0.1578 0.9909
01.03 nucleotide/nucleoside/nucleobase metabolism 0.6538 0.3523 0.9892 0.4579 0.9543
01.03.01 purin nucleotide/nucleoside/nucleobase metabolism 0.7187 0.4035 0.9974 0.5168 0.9878
01.03.01.03 purine nucleotide/nucleoside/nucleobase anabolism 0.6153 0.2857 0.9985 0.3902 0.9929
01.03.04 pyrimidine nucleotide/nucleoside/nucleobase metabolism 0.6333 0.4222 0.9968 0.5066 0.9895
01.03.16 polynucleotide degradation 0.5277 0.2714 0.9950 0.3584 0.9807
01.03.16.01 RNA degradation 0.5416 0.2888 0.9968 0.3768 0.9878
01.04 phosphate metabolism 0.8134 0.6083 0.9852 0.6960 0.9492
01.05 C-compound and carbohydrate metabolism 0.7869 0.5010 0.9798 0.6122 0.9178
01.05.02 sugar, glucoside, polyol and carboxylate metabolism 0.6500 0.3513 0.9959 0.4561 0.9824
01.05.02.04 sugar, glucoside, polyol and carboxylate anabolism 0.5500 0.3333 0.9974 0.4150 0.9912
01.05.02.07 sugar, glucoside, polyol and carboxylate catabolism 1.0000 0.0972 1.0000 0.1772 0.9815
01.05.03 polysaccharide metabolism 0.7777 0.2500 0.9988 0.3783 0.9869
01.05.25 regulation of C-compound and carbohydrate metabolism 0.4750 0.1570 0.9938 0.2360 0.9651
01.06 lipid, fatty acid and isoprenoid metabolism 0.7536 0.4444 0.9896 0.5591 0.9535
01.06.02 membrane lipid metabolism 0.7647 0.4126 0.9976 0.5360 0.9872
01.06.02.01 phospholipid metabolism 0.6896 0.3636 0.9974 0.4761 0.9875
01.06.05 fatty acid metabolism 0.4285 0.1500 0.9988 0.2222 0.9940
01.06.06 isoprenoid metabolism 0.6500 0.3421 0.9979 0.4482 0.9909
01.06.06.11 tetracyclic and pentacyclic triterpenes metabolism 0.6153 0.2352 0.9985 0.3404 0.9912
01.06.10 regulation of lipid, fatty acid and isoprenoid metabolism 0.8571 0.2400 0.9997 0.3750 0.9943
01.07 metabolism of vitamins, cofactors, and prosthetic groups 0.7454 0.2887 0.9958 0.4162 0.9674
01.07.01 biosynthesis of vitamins, cofactors, and prosthetic groups 0.7209 0.3195 0.9965 0.4428 0.9778
01.20 secondary metabolism 0.8000 0.1142 0.9994 0.2000 0.9818

Tab. 3 shows the results obtained by TPR-w ensembles using Sequence similarity (SP-sim) data.



Table 3: Classification results on the FunCat tree rooted at "Metabolism" using SP-sim data. Each row represents a functional class of the FunCat taxonomy. Prec. stands for precision, Rec. recall, Sp. specificity, F F-measure, Acc. accuracy.
FunCat ID Description Prec. Rec. Sp. F Acc.
01 Metabolism 0.8342 0.5802 0.9340 0.6844 0.8053
01.01 amino acid metabolism 0.6481 0.3083 0.9884 0.4179 0.9447
01.01.03 assimilation of ammonia, metabolism of the glutamate group 0.3043 0.1521 0.9954 0.2028 0.9844
01.01.03.02 metabolism of glutamate 0.4375 0.3181 0.9974 0.3684 0.9931
01.01.03.05 metabolism of arginine 0.0000 0.0000 0.9982 0.0000 0.9923
01.01.06 metabolism of the aspartate family 0.4642 0.2166 0.9956 0.2954 0.9824
01.01.06.05 metabolism of methionine 0.7500 0.2903 0.9991 0.4186 0.9929
01.01.09 metabolism of the cysteine - aromatic group 0.5151 0.2207 0.9953 0.3090 0.9784
01.01.13 regulation of amino acid metabolism 0.2000 0.0322 0.9988 0.0555 0.9903
01.02 nitrogen, sulfur and selenium metabolism 0.5925 0.1882 0.9968 0.2857 0.9773
01.02.07 regulation of nitrogen, sulfur and selenium metabolism 0.2857 0.0740 0.9985 0.1176 0.9914
01.03 nucleotide/nucleoside/nucleobase metabolism 0.6630 0.3160 0.9907 0.4280 0.9538
01.03.01 purin nucleotide/nucleoside/nucleobase metabolism 0.8400 0.3684 0.9988 0.5121 0.9886
01.03.01.03 purine nucleotide/nucleoside/nucleobase anabolism 0.5833 0.2500 0.9985 0.3500 0.9926
01.03.04 pyrimidine nucleotide/nucleoside/nucleobase metabolism 0.6296 0.3777 0.9971 0.4722 0.9892
01.03.16 polynucleotide degradation 0.5757 0.2714 0.9959 0.3689 0.9815
01.03.16.01 RNA degradation 0.5909 0.2888 0.9974 0.3880 0.9883
01.04 phosphate metabolism 0.8218 0.6023 0.9862 0.6952 0.9495
01.05 C-compound and carbohydrate metabolism 0.7943 0.4901 0.9811 0.6062 0.9175
01.05.02 sugar, glucoside, polyol and carboxylate metabolism 0.6315 0.3243 0.9959 0.4285 0.9818
01.05.02.04 sugar, glucoside, polyol and carboxylate anabolism 0.5000 0.2727 0.9974 0.3529 0.9906
01.05.02.07 sugar, glucoside, polyol and carboxylate catabolism 1.0000 0.0972 1.0000 0.1772 0.9815
01.05.03 polysaccharide metabolism 0.7777 0.2500 0.9988 0.3783 0.9869
01.05.25 regulation of C-compound and carbohydrate metabolism 0.4545 0.1239 0.9947 0.1948 0.9648
01.06 lipid, fatty acid and isoprenoid metabolism 0.7555 0.4358 0.9899 0.5528 0.9532
01.06.02 membrane lipid metabolism 0.7878 0.4126 0.9979 0.5416 0.9875
01.06.02.01 phospholipid metabolism 0.7142 0.3636 0.9976 0.4819 0.9878
01.06.05 fatty acid metabolism 0.4285 0.1500 0.9988 0.2222 0.9940
01.06.06 isoprenoid metabolism 0.6666 0.3157 0.9982 0.4285 0.9909
01.06.06.11 tetracyclic and pentacyclic triterpenes metabolism 0.5833 0.2058 0.9985 0.3043 0.9909
01.06.10 regulation of lipid, fatty acid and isoprenoid metabolism 0.8571 0.2400 0.9997 0.3750 0.9943
01.07 metabolism of vitamins, cofactors, and prosthetic groups 0.8260 0.2676 0.9976 0.4042 0.9682
01.07.01 biosynthesis of vitamins, cofactors, and prosthetic groups 0.8235 0.2886 0.9982 0.4274 0.9787
01.20 secondary metabolism 0.8000 0.1142 0.9994 0.2000 0.9818

Tab. 4 shows the results obtained by TPR-w ensembles using the Gene expression data.



Table 4: Classification results on the FunCat tree rooted at "Metabolism" using Gene expression data. Each row represents a functional class of the FunCat taxonomy. Prec. stands for precision, Rec. recall, Sp. specificity, F F-measure, Acc. accuracy.
FunCat ID Description Prec. Rec. Sp. F Acc.
01 Metabolism 0.4719 0.4913 0.7260 0.4814 0.6480
01.01 amino acid metabolism 0.3718 0.4256 0.9593 0.3969 0.9307
01.01.03 assimilation of ammonia, metabolism of the glutamate group 0.1344 0.3478 0.9769 0.1939 0.9705
01.01.03.02 metabolism of glutamate 0.0923 0.2608 0.9868 0.1363 0.9831
01.01.03.05 metabolism of arginine 0.1320 0.3500 0.9897 0.1917 0.9869
01.01.06 metabolism of the aspartate family 0.2967 0.4090 0.9856 0.3439 0.9772
01.01.06.05 metabolism of methionine 0.2241 0.3714 0.9899 0.2795 0.9851
01.01.09 metabolism of the cysteine - aromatic group 0.2222 0.2716 0.9826 0.2444 0.9699
01.01.09.06 metabolism of tryptophan 0.0816 0.2000 0.9900 0.1159 0.9865
01.01.13 regulation of amino acid metabolism 0.0000 0.0000 0.9942 0.0000 0.9871
01.02 nitrogen, sulfur and selenium metabolism 0.2500 0.2395 0.9844 0.2446 0.9686
01.02.07 regulation of nitrogen, sulfur and selenium metabolism 0.0833 0.0666 0.9951 0.0740 0.9889
01.03 nucleotide/nucleoside/nucleobase metabolism 0.1246 0.2262 0.9184 0.1607 0.8845
01.03.01 purin nucleotide/nucleoside/nucleobase metabolism 0.1800 0.3000 0.9816 0.2250 0.9725
01.03.01.03 purine nucleotide/nucleoside/nucleobase anabolism 0.2790 0.4137 0.9931 0.3333 0.9893
01.03.04 pyrimidine nucleotide/nucleoside/nucleobase metabolism 0.1267 0.1875 0.9861 0.1512 0.9776
01.03.16 polynucleotide degradation 0.0352 0.0952 0.9506 0.0514 0.9347
01.03.16.01 RNA degradation 0.0428 0.1153 0.9700 0.0625 0.9602
01.04 phosphate metabolism 0.1497 0.1411 0.9183 0.1453 0.8465
01.05 C-compound and carbohydrate metabolism 0.2353 0.3200 0.8699 0.2712 0.8087
01.05.02 sugar, glucoside, polyol and carboxylate metabolism 0.1567 0.2592 0.9745 0.1953 0.9617
01.05.02.04 sugar, glucoside, polyol and carboxylate anabolism 0.0600 0.0857 0.9895 0.0705 0.9825
01.05.02.07 sugar, glucoside, polyol and carboxylate catabolism 0.1142 0.1012 0.9860 0.1073 0.9705
01.05.03 polysaccharide metabolism 0.0975 0.1250 0.9834 0.1095 0.9712
01.05.13 transfer of activated C-1 groups 0.2105 0.2000 0.9966 0.2051 0.9931
01.05.25 regulation of C-compound and carbohydrate metabolism 0.0632 0.1259 0.9460 0.0842 0.9230
01.06 lipid, fatty acid and isoprenoid metabolism 0.1528 0.2007 0.9254 0.1735 0.8799
01.06.02 membrane lipid metabolism 0.0357 0.0487 0.9756 0.0412 0.9588
01.06.02.01 phospholipid metabolism 0.0769 0.0294 0.9946 0.0425 0.9801
01.06.05 fatty acid metabolism 0.0218 0.1666 0.9602 0.0386 0.9560
01.06.06 isoprenoid metabolism 0.1944 0.3414 0.9870 0.2477 0.9812
01.06.06.11 tetracyclic and pentacyclic triterpenes metabolism 0.1612 0.2777 0.9884 0.2040 0.9827
01.06.10 regulation of lipid, fatty acid and isoprenoid metabolism 0.0277 0.2000 0.9610 0.0487 0.9568
01.07 metabolism of vitamins, cofactors, and prosthetic groups 0.1261 0.1646 0.9571 0.1428 0.9283
01.07.01 biosynthesis of vitamins, cofactors, and prosthetic groups 0.0649 0.0909 0.9673 0.0757 0.9460
01.20 secondary metabolism 0.1521 0.0921 0.9912 0.1147 0.9761

FunCat ID 10: Cell cycle and DNA processing

Fig. 3 represents the FunCat tree rooted at the functional class "Cell cycle and DNA processing".
Figure 3: Tree of the FunCat classes rooted at Funcat ID=10 (Cell cycle and DNA processing).
\includegraphics[width = 18cm]{eps/tree.10.eps}

Tab. 5 shows the results obtained by TPR-w ensembles with SP-sim data.



Table 5: Classification results on the FunCat tree rooted at "Cell cycle and DNA processing", using SP-sim data. Each row represents a functional class of the FunCat taxonomy. Prec. stands for precision, Rec. recall, Sp. specificity, F F-measure, Acc. accuracy.
FunCat ID Description Prec. Rec. Sp. F Acc.
10 Cell cycle and DNA processing 0.7493 0.4033 0.9622 0.5244 0.8401
10.01 DNA processing 0.6931 0.3236 0.9828 0.4412 0.9124
10.01.02 DNA topology 0.7333 0.3333 0.9988 0.4583 0.9926
10.01.03 DNA synthesis and replication 0.5609 0.2053 0.9947 0.3006 0.9696
10.01.03.03 ori recognition and priming complex formation 1.0000 0.2500 1.0000 0.4000 0.9948
10.01.03.05 extension/ polymerization activity 0.5000 0.2285 0.9977 0.3137 0.9900
10.01.05 DNA recombination and DNA repair 0.5257 0.2537 0.9861 0.3422 0.9444
10.01.05.01 DNA repair 0.4698 0.2910 0.9870 0.3594 0.9606
10.01.05.03 DNA recombination 0.6315 0.1818 0.9979 0.2823 0.9827
10.01.05.03.01 meiotic recombination 0.3750 0.1000 0.9985 0.1578 0.9909
10.01.09 DNA restriction or modification 0.6521 0.3103 0.9929 0.4205 0.9648
10.01.09.05 DNA conformation modification (e.g. chromatin) 0.6567 0.3283 0.9932 0.4378 0.9679
10.03 cell cycle 0.6305 0.3707 0.9612 0.4669 0.8719
10.03.01 mitotic cell cycle and cell cycle control 0.5434 0.3816 0.9598 0.4484 0.8954
10.03.01.01 mitotic cell cycle 0.4857 0.2463 0.9893 0.3269 0.9603
10.03.01.01.03 G1/S transition of mitotic cell cycle 0.7272 0.2500 0.9991 0.3720 0.9923
10.03.01.01.09 G2/M transition of mitotic cell cycle 0.4705 0.1904 0.9974 0.2711 0.9878
10.03.01.01.11 M phase 0.4000 0.2222 0.9956 0.2857 0.9858
10.03.01.03 cell cycle checkpoints 0.3333 0.0943 0.9971 0.1470 0.9835
10.03.02 meiosis 0.4000 0.0967 0.9947 0.1558 0.9631
10.03.03 cytokinesis /septum formation and hydrolysis 0.4736 0.1500 0.9971 0.2278 0.9827
10.03.04 nuclear and chromosomal cycle 0.5000 0.1139 0.9973 0.1855 0.9776
10.03.04.03 chromosome condensation 0.6666 0.2000 0.9994 0.3076 0.9948
10.03.04.05 chromosome segregation/division 0.4285 0.0833 0.9988 0.1395 0.9895
10.03.05 cell cycle dependent cytoskeleton reorganization 0.0257 0.1515 0.9459 0.0440 0.9385
10.03.05.01 spindle pole body/centrosome and microtubule cycle 0.0133 0.0384 0.9788 0.0198 0.9719

Tab. 6 shows the results obtained by TPR-w ensembles with gene expression data.



Table 6: Classification results on the FunCat tree rooted at "Cell cycle and DNA processing", using gene expression data. Each row represents a functional class of the FunCat taxonomy. Prec. stands for precision, Rec. recall, Sp. specificity, F F-measure, Acc. accuracy.
FunCat ID Description Prec. Rec. Sp. F Acc.
10 Cell cycle and DNA processing 0.4111 0.4208 0.8335 0.4159 0.7441
10.01 DNA processing 0.2656 0.3915 0.8660 0.3165 0.8138
10.01.02 DNA topology 0.3469 0.3207 0.9928 0.3333 0.9849
10.01.03 DNA synthesis and replication 0.1182 0.1641 0.9626 0.1375 0.9389
10.01.03.03 ori recognition and priming complex formation 0.1020 0.2000 0.9902 0.1351 0.9858
10.01.03.05 extension/ polymerization activity 0.0606 0.1052 0.9861 0.0769 0.9787
10.01.05 DNA recombination and DNA repair 0.1506 0.2796 0.9132 0.1958 0.8801
10.01.05.01 DNA repair 0.1100 0.2142 0.9388 0.1453 0.9142
10.01.05.03 DNA recombination 0.0792 0.2000 0.9581 0.1134 0.9447
10.01.05.03.01 meiotic recombination 0.0610 0.2222 0.9725 0.0958 0.9666
10.01.05.03.03 somatic / mitotic recombination 0.0666 0.0952 0.9937 0.0784 0.9896
10.01.09 DNA restriction or modification 0.1103 0.3246 0.8845 0.1646 0.8609
10.01.09.05 DNA conformation modification (e.g. chromatin) 0.1050 0.2918 0.8939 0.1545 0.8693
10.03 cell cycle 0.2774 0.3537 0.8492 0.3109 0.7795
10.03.01 mitotic cell cycle and cell cycle control 0.1951 0.2794 0.8779 0.2298 0.8206
10.03.01.01 mitotic cell cycle 0.1080 0.2187 0.9337 0.1446 0.9084
10.03.01.01.01 G1 phase of mitotic cell cycle 0.0194 0.0952 0.9775 0.0322 0.9734
10.03.01.01.03 G1/S transition of mitotic cell cycle 0.0246 0.0540 0.9823 0.0338 0.9747
10.03.01.01.09 G2/M transition of mitotic cell cycle 0.0689 0.1250 0.9818 0.0888 0.9728
10.03.01.01.11 M phase 0.0813 0.1428 0.9823 0.1037 0.9732
10.03.01.02 cell cycle arrest 0.0000 0.0000 0.9435 0.0000 0.9394
10.03.01.03 cell cycle checkpoints 0.0666 0.0625 0.9874 0.0645 0.9743
10.03.02 meiosis 0.1264 0.1401 0.9651 0.1329 0.9365
10.03.03 cytokinesis (cell division) /septum formation and hydrolysis 0.1166 0.0985 0.9880 0.1068 0.9741
10.03.04 nuclear and chromosomal cycle 0.0947 0.2547 0.9415 0.1381 0.9254
10.03.04.03 chromosome condensation 0.1282 0.2272 0.9924 0.1639 0.9887
10.03.04.05 chromosome segregation/division 0.0596 0.2363 0.9541 0.0952 0.9453
10.03.05 cell cycle dependent cytoskeleton reorganization 0.0349 0.2291 0.9320 0.0606 0.9246
10.03.05.01 spindle pole body/centrosome and microtubule cycle 0.0369 0.2682 0.9359 0.0648 0.9299

FunCat ID 12: Protein synthesis

Fig. 4 represents the FunCat tree rooted at the functional class "Protein synthesis".
Figure 4: Tree of the FunCat classes rooted at Funcat ID=12 (Protein synthesis).
\includegraphics[width = 10cm]{eps/tree.12.eps}

Tab. 7 shows the results obtained by TPR-w ensembles with Gene expression data.



Table 7: Classification results on the FunCat tree rooted at "Protein synthesis", using Gene expression data. Each row represents a functional class of the FunCat taxonomy. Prec. stands for precision, Rec. recall, Sp. specificity, F F-measure, Acc. accuracy.
FunCat ID Description Prec. Rec. Sp. F Acc.
12 Protein synthesis 0.5945 0.6230 0.9520 0.6085 0.9186
12.01 ribosome biogenesis 0.6043 0.7689 0.9655 0.6767 0.9529
12.01.01 ribosomal proteins 0.6462 0.7920 0.9771 0.7117 0.9679
12.04 translation 0.1707 0.1627 0.9846 0.1666 0.9690
12.04.01 translation initiation 0.0322 0.0250 0.9933 0.0281 0.9847
12.04.02 translation elongation 0.3333 0.2857 0.9973 0.3076 0.9940
12.07 translational control 0.0645 0.0363 0.9935 0.0465 0.9818
12.10 aminoacyl-tRNA-synthetases 0.5161 0.4102 0.9966 0.4571 0.9915

Tab. 8 shows the results obtained by TPR-w ensembles with Pfam-1 data.



Table 8: Classification results on the FunCat tree rooted at "Protein synthesis", using Pfam-1 data. Each row represents a functional class of the FunCat taxonomy. Prec. stands for precision, Rec. recall, Sp. specificity, F F-measure, Acc. accuracy.
FunCat ID Description Prec. Rec. Sp. F Acc.
12 Protein synthesis 0.8969 0.37659 0.9945 0.5304 0.9257
12.01 ribosome biogenesis 0.8787 0.36250 0.9963 0.5132 0.9532
12.01.01 ribosomal proteins 0.8585 0.41871 0.9957 0.5629 0.9625
12.04 translation 0.9696 0.40000 0.9997 0.5663 0.9861
12.04.01 translation initiation 1.0000 0.16216 1.0000 0.2790 0.9912
12.04.02 translation elongation 0.8000 0.76190 0.9988 0.7804 0.9974
12.07 translational control 0.0156 0.02040 0.9818 0.0176 0.9685
12.10 aminoacyl-tRNA-synthetases 1.0000 0.74358 1.0000 0.8529 0.9971

FunCat ID 14: Protein fate

Fig. 5 represents the FunCat tree rooted at the functional class "Protein fate". With this specific subtree (such as with other specific subtrees), using the Pfam-1 data set, TPR-w ensembles obtain high precision/recall rates with most of the classes of the tree (Tab. 9).

Figure 5: Tree of the FunCat classes rooted at Funcat ID=14 (Protein fate).
\includegraphics[width = 10cm]{eps/tree.14.eps}



Table 9: Classification results on the FunCat tree rooted at "Protein fate", using Pfam-1 data. Each row represents a functional class of the FunCat taxonomy. Prec. stands for precision, Rec. recall, Sp. specificity, F F-measure, Acc. accuracy.
FunCat ID Description Prec. Rec. Sp. F Acc.
14 Protein fate (folding, modification, destination) 0.8342 0.5182 0.9645 0.6393 0.8503
14.01 protein folding and stabilization 0.8437 0.6585 0.9970 0.7397 0.9892
14.04 protein targeting, sorting and translocation 0.6224 0.2760 0.9888 0.3824 0.9441
14.07 protein modification 0.8287 0.5753 0.9816 0.6791 0.9274
14.07.01 modification with fatty acids 0.8333 0.2083 0.9997 0.3333 0.9943
14.07.02 modification with sugar residues 0.9090 0.4615 0.9991 0.6122 0.9892
14.07.02.02 N-directed glycosylation, deglycosylation 0.7826 0.4390 0.9985 0.5625 0.9920
14.07.03 modification by phosphorylation 0.8717 0.7445 0.9955 0.8031 0.9858
14.07.04 modification by acetylation 0.8823 0.3061 0.9994 0.4545 0.9897
14.07.05 modification by ubiquitination 0.8846 0.6865 0.9982 0.7731 0.9923
14.07.11 protein processing (proteolytic) 0.7142 0.3846 0.9971 0.5000 0.9858
14.10 assembly of protein complexes 0.7555 0.2048 0.9967 0.3222 0.9594
14.13 protein/peptide degradation 0.7986 0.5609 0.9912 0.6590 0.9662
14.13.01 cytoplasmic and nuclear protein degradation 0.6940 0.5886 0.9878 0.6369 0.9699
14.13.01.01 proteasomal degradation 0.6629 0.5619 0.9912 0.6082 0.9784

Tab. 10 shows the results obtained by TPR-w ensembles using Sequence similarity (SP-sim) data.



Table 10: Classification results on the FunCat tree rooted at "Protein fate", using SP-sim data. Each row represents a functional class of the FunCat taxonomy. Prec. stands for precision, Rec. recall, Sp. specificity, F F-measure, Acc. accuracy.
FunCat ID Description Prec. Rec. Sp. F Acc.
14 Protein fate (folding, modification, destination) 0.8360 0.5083 0.9657 0.6322 0.8486
14.01 protein folding and stabilization 0.8437 0.6585 0.9970 0.7397 0.9892
14.04 protein targeting, sorting and translocation 0.6105 0.2624 0.9888 0.3670 0.9433
14.07 protein modification 0.8364 0.5647 0.9829 0.6742 0.9271
14.07.01 modification with fatty acids 0.8333 0.2083 0.9997 0.3333 0.9943
14.07.02 modification with sugar residues 0.9062 0.4461 0.9991 0.5979 0.9889
14.07.02.02 N-directed glycosylation, deglycosylation 0.7727 0.4146 0.9985 0.5396 0.9917
14.07.03 modification by phosphorylation 0.8717 0.7445 0.9955 0.8031 0.9858
14.07.04 modification by acetylation 0.8823 0.3061 0.9994 0.4545 0.9897
14.07.05 modification by ubiquitination 0.9019 0.6865 0.9985 0.7796 0.9926
14.07.11 protein processing (proteolytic) 0.7352 0.3846 0.9974 0.5050 0.9861
14.10 assembly of protein complexes 0.7727 0.2048 0.9970 0.3238 0.9597
14.13 protein/peptide degradation 0.8028 0.5560 0.9915 0.6570 0.9662
14.13.01 cytoplasmic and nuclear protein degradation 0.6946 0.5759 0.9881 0.6297 0.9696
14.13.01.01 proteasomal degradation 0.6860 0.5619 0.9921 0.6178 0.9793

FunCat ID 16: Protein with binding function or cofactor requirement

Fig. 6 represents the FunCat tree rooted at the functional class "Protein with binding function or cofactor requirement". Tab. 11 show the results obtained by TPR-w ensembles with the Pfam-1 data set
Figure 6: Tree of the FunCat classes rooted at Funcat ID=16 (Protein with binding function or cofactor requirement).
\includegraphics[width = 10cm]{eps/tree.16.eps}



Table 11: Classification results on the FunCat tree rooted at "Protein with binding function or cofactor requirement", using Pfam-1 data. Each row represents a functional class of the FunCat taxonomy. Prec. stands for precision, Rec. recall, Sp. specificity, F F-measure, Acc. accuracy.
FunCat ID Description Prec. Rec. Sp. F Acc.
16 Protein with binding function or cofactor requirement 0.6894 0.3988 0.9443 0.5053 0.8152
16.01 protein binding 0.5923 0.3069 0.9801 0.4043 0.9223
16.03 nucleic acid binding 0.6666 0.3471 0.9859 0.4565 0.9379
16.03.01 DNA binding 0.6060 0.2941 0.9923 0.3960 0.9654
16.03.03 RNA binding 0.7123 0.3880 0.9938 0.5024 0.9708
16.07 structural protein binding 0.8333 0.1923 0.9994 0.3125 0.9875
16.19 nucleotide/nucleoside/nucleobase binding 0.6269 0.5990 0.9783 0.6126 0.9566
16.19.03 ATP binding 0.6129 0.6589 0.9785 0.6350 0.9628
16.21 complex cofactor/cosubstrate/vitamine binding 0.7200 0.3529 0.9979 0.4736 0.9886
16.21.07 NAD/NADP binding 0.8095 0.5000 0.9988 0.6181 0.9940

Tab. 12 show the results obtained by TPR-w ensembles with the Pfam-1 data set



Table 12: Classification results on the FunCat tree rooted at "Protein with binding function or cofactor requirement", using PPI Biogrid data. Each row represents a functional class of the FunCat taxonomy. Prec. stands for precision, Rec. recall, Sp. specificity, F F-measure, Acc. accuracy.
FunCat ID Description Prec. Rec. Sp. F Acc.
16 Protein with binding function or cofactor requirement 0.7082 0.3808 0.9513 0.4953 0.8163
16.01 protein binding 0.6258 0.2871 0.9838 0.3936 0.9240
16.03 nucleic acid binding 0.6842 0.3433 0.9871 0.4572 0.9387
16.03.01 DNA binding 0.6451 0.2941 0.9935 0.4040 0.9665
16.03.03 RNA binding 0.7083 0.3805 0.9938 0.4951 0.9705
16.07 structural protein binding 0.8333 0.1923 0.9994 0.3125 0.9875
16.19 nucleotide/nucleoside/nucleobase binding 0.6746 0.5544 0.9837 0.6086 0.9591
16.19.03 ATP binding 0.6603 0.6069 0.9839 0.6325 0.9654
16.21 complex cofactor/cosubstrate/vitamine binding 0.7500 0.3529 0.9982 0.4800 0.9889
16.21.07 NAD/NADP binding 0.8500 0.5000 0.9991 0.6296 0.9943

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