PENCE PENCE Proteome Analyst

Custom Classifiers:




Table 1: Confusion matrix for K Ion
Prd ⇒
Obs ⇓		 Predicted as
Kv4		 Predicted as
Kv3		 Predicted as
Kv2		 Predicted as
Kv1		 No Prediction Row Sum Recall
Kv4
in training set		 19 0 0 0 0 19 1.000
Kv3
in training set		 0 17 0 0 0 17 1.000
Kv2
in training set		 0 0 17 0 0 17 1.000
Kv1
in training set		 0 0 0 24 0 24 1.000
Col Sum 19 17 17 24 0 77 Overall
Recall
= 1.000
Precision 1.000 1.000 1.000 1.000 Sequence
Coverage
= 1.000		 - Overall
Precision
= 1.000
Specificity 1.000 1.000 1.000 1.000 - - Overall
Specificity
= 1.000


Table 2: Confusion matrix for Gene Ontology Funtion
Prd ⇒
Obs ⇓		 Predicted as
positive		 Predicted as
negative 		No Predictions RowSum Precision Recall
hydrolase activity (0016787) Positive in
training set 		16866 485 17 17368 0.8947005 0.9710963
Negative in
training set		 1985 82778 94 84857
signal transducer activity (0004871) Positive in
training set 		7609 316 8 7933 0.7987613 0.95915794
Negative in
training set		 1917 92272 103 94292
metal ion binding (0046872) Positive in
training set 		9533 517 3 10053 0.7773791 0.94827414
Negative in
training set		 2730 89334 108 92172
lyase activity (0016829) Positive in
training set 		5712 105 4 5821 0.8895811 0.9812747
Negative in
training set		 709 95588 107 96404
binding (0005488) Positive in
training set 		47901 2792 57 50750 0.95734984 0.9438621
Negative in
training set		 2134 49287 54 51475
structural molecule activity (0005198) Positive in
training set 		7478 252 13 7743 0.9701609 0.96577555
Negative in
training set		 230 94154 98 94482
transporter activity (0005215) Positive in
training set		 13773 430 7 14210 0.8607049 0.969247
Negative in
training set		 2229 85682 104 88015
transferase activity (0016740) Positive in
training set		 17565 378 7 17950 0.9566472 0.9785515
Negative in
training set		 796 83375 104 84275
catalytic activity (0003824) Positive in
training set 		59974 1219 49 61242 0.9824073 0.97929525
Negative in
training set 		1074 39847 62 40983
nucleic acid binding (0003676) Positive in
training set		 20454 573 28 21055 0.8916692 0.9714557
Negative in
training set 		2485 78602 83 81170
oxidoreductase activity (0016491) Positive in
training set		 10754 154 5 10913 0.8781643 0.98543024
Negative in
training set 		1492 89714 106 91312
nucleotide binding (0000166) Positive in
training set 		15995 251 5 16251 0.9603146 0.98424715
Negative in
training set 		661 85207 106 85974
Overall Positive in
training set		 233614 7472 203 241289 0.92683375 0.9690069
Negative in
training set 		18442 965840 1129 985411


Table 3: Confusion matrix for Gene Quiz - Multi
Prd ⇒
Obs ⇓		 Predicted as
Energy metabolism		 Predicted as
Replication		 Predicted as
Translation		 Predicted as
Regulatory functions		 Predicted as
Cellular processes		 Predicted as
Central intermediary metabolism		 Predicted as
Transcription		 Predicted as
Cell envelope		 Predicted as
Other categories		 Predicted as
Biosynthesis of cofactors		 Predicted as
Purines		 Predicted as
Transport and binding proteins		 Predicted as
Amino acid biosynthesis		 Predicted as
Fatty acid and phospholipid metabolism		 No Prediction Row Sum Recall
Energy metabolism
in training set		 819 2 8 1 2 13 1 7 2 6 27 6 13 3 4 914 0.896
Replication
in training set		 1 358 2 32 7 6 32 4 7 15 30 1 7 5 19 526 0.681
Translation
in training set		 0 5 518 0 3 0 7 10 0 1 4 1 0 3 11 563 0.920
Regulatory functions
in training set		 7 28 16 768 20 3 46 9 7 3 63 19 1 8 25 1023 0.751
Cellular processes
in training set		 14 20 12 4 659 5 5 13 8 3 7 20 3 6 12 791 0.833
Central intermediary metabolism
in training set		 4 1 4 1 15 385 1 7 1 5 22 12 22 5 9 494 0.779
Transcription
in training set		 4 31 20 71 30 8 444 4 25 7 22 12 3 0 12 693 0.641
Cell envelope
in training set		 8 7 6 3 25 25 9 396 0 2 10 46 5 7 30 579 0.684
Other categories
in training set		 3 2 1 1 3 0 11 1 72 2 0 5 0 0 3 104 0.692
Biosynthesis of cofactors
in training set		 17 5 2 3 3 7 2 1 0 147 10 5 14 3 0 219 0.671
Purines
in training set		 11 24 10 14 12 26 5 18 1 4 580 36 13 9 5 768 0.755
Transport and binding proteins
in training set		 4 22 6 5 24 38 4 116 9 5 35 1267 5 10 28 1578 0.803
Amino acid biosynthesis
in training set		 4 0 0 0 2 4 0 1 0 7 6 3 228 8 3 266 0.857
Fatty acid and phospholipid metabolism
in training set		 8 4 1 2 1 3 3 2 0 0 4 1 10 194 3 236 0.822
Col Sum 904 509 606 905 806 523 570 589 132 207 820 1434 324 261 164 8754 Overall
Recall
= 0.781
Precision 0.906 0.703 0.855 0.849 0.818 0.736 0.779 0.672 0.545 0.710 0.707 0.884 0.704 0.743 Sequence
Coverage
= 0.981		 - Overall
Precision
= 0.796
Specificity 0.989 0.982 0.989 0.982 0.982 0.983 0.984 0.976 0.993 0.993 0.970 0.977 0.989 0.992 - - Overall
Specificity
= 0.982


Table 4: Confusion matrix for Gene Quiz - Fly
Prd ⇒
Obs ⇓		 Predicted as
Energy metabolism		 Predicted as
Replication		 Predicted as
Translation		 Predicted as
Cellular processes		 Predicted as
Regulatory functions		 Predicted as
Central intermediary metabolism		 Predicted as
Transcription		 Predicted as
Cell envelope		 Predicted as
Other categories		 Predicted as
Biosynthesis of cofactors		 Predicted as
Purines		 Predicted as
Transport and binding proteins		 Predicted as
Amino acid biosynthesis		 Predicted as
Fatty acid and phospholipid metabolism		 No Prediction Row Sum Recall
Energy metabolism
in training set		 309 0 5 4 0 6 0 6 0 9 9 2 1 6 3 360 0.858
Replication
in training set		 0 102 0 6 21 1 13 1 2 5 14 2 1 4 2 174 0.586
Translation
in training set		 0 2 212 3 0 0 4 4 0 1 2 0 0 2 0 230 0.922
Cellular processes
in training set		 7 5 5 258 2 2 5 1 4 4 6 8 1 2 4 314 0.822
Regulatory functions
in training set		 3 14 9 10 289 0 33 0 1 6 32 15 0 6 7 425 0.680
Central intermediary metabolism
in training set		 1 0 2 10 0 161 3 1 0 1 13 5 7 1 3 208 0.774
Transcription
in training set		 0 13 14 21 50 3 231 1 22 6 11 10 1 1 9 393 0.588
Cell envelope
in training set		 4 4 5 18 0 5 2 159 2 0 8 11 2 2 14 236 0.674
Other categories
in training set		 1 2 0 1 1 0 6 0 19 0 0 1 0 0 0 31 0.613
Biosynthesis of cofactors
in training set		 7 1 3 3 3 1 2 0 0 56 5 3 7 5 0 96 0.583
Purines
in training set		 5 18 10 13 11 16 5 15 1 1 294 29 10 3 2 433 0.679
Transport and binding proteins
in training set		 4 2 1 14 6 28 2 79 2 1 21 627 2 4 9 802 0.782
Amino acid biosynthesis
in training set		 5 0 0 1 0 0 0 0 0 5 2 1 29 0 0 43 0.674
Fatty acid and phospholipid metabolism
in training set		 6 1 2 1 1 1 1 0 0 3 4 0 3 73 1 97 0.753
Col Sum 352 164 268 363 384 224 307 267 53 98 421 714 64 109 54 3842 Overall
Recall
= 0.734
Precision 0.878 0.622 0.791 0.711 0.753 0.719 0.752 0.596 0.358 0.571 0.698 0.878 0.453 0.670 Sequence
Coverage
= 0.986		 - Overall
Precision
= 0.744
Specificity 0.988 0.983 0.984 0.970 0.972 0.983 0.978 0.970 0.991 0.989 0.963 0.971 0.991 0.990 - - Overall
Specificity
= 0.976


Table 5: Confusion matrix for Gene Quiz - E.coli
Prd ⇒
Obs ⇓		 Predicted as
Energy metabolism		 Predicted as
Replication		 Predicted as
Translation		 Predicted as
Cellular processes		 Predicted as
Regulatory functions		 Predicted as
Central intermediary metabolism		 Predicted as
Transcription		 Predicted as
Cell envelope		 Predicted as
Other categories		 Predicted as
Biosynthesis of cofactors		 Predicted as
Purines		 Predicted as
Transport and binding proteins		 Predicted as
Amino acid biosynthesis		 Predicted as
Fatty acid and phospholipid metabolism		 No Prediction Row Sum Recall
Energy metabolism
in training set		 293 0 1 1 0 2 0 0 0 4 18 7 5 1 1 333 0.880
Replication
in training set		 3 116 0 0 3 5 8 1 0 4 2 0 1 1 8 152 0.763
Translation
in training set		 0 1 91 1 0 1 2 0 0 0 1 2 0 1 2 102 0.892
Cellular processes
in training set		 5 1 3 92 1 2 0 6 5 0 0 2 0 0 3 120 0.767
Regulatory functions
in training set		 1 6 3 5 266 5 0 5 0 0 3 4 1 0 9 308 0.864
Central intermediary metabolism
in training set		 0 2 2 3 0 86 0 10 1 1 5 5 8 2 3 128 0.672
Transcription
in training set		 0 11 1 1 0 1 37 0 0 0 5 1 1 0 1 59 0.627
Cell envelope
in training set		 3 0 0 5 4 13 2 183 2 3 5 16 1 5 12 254 0.720
Other categories
in training set		 1 0 0 3 0 0 0 1 21 2 0 1 0 0 0 29 0.724
Biosynthesis of cofactors
in training set		 8 3 0 1 0 5 0 1 2 38 4 2 10 1 0 75 0.507
Purines
in training set		 6 2 0 1 2 3 0 2 0 2 90 3 3 8 1 123 0.732
Transport and binding proteins
in training set		 5 23 2 2 0 5 0 11 2 4 2 416 1 4 8 485 0.858
Amino acid biosynthesis
in training set		 5 0 1 0 0 3 1 0 0 2 6 1 101 5 3 128 0.789
Fatty acid and phospholipid metabolism
in training set		 1 1 1 0 1 2 0 2 0 0 3 1 5 60 0 77 0.779
Col Sum 331 166 105 115 277 133 50 222 33 60 144 461 137 88 51 2373 Overall
Recall
= 0.796
Precision 0.885 0.699 0.867 0.800 0.960 0.647 0.740 0.824 0.636 0.633 0.625 0.902 0.737 0.682 Sequence
Coverage
= 0.979		 - Overall
Precision
= 0.814
Specificity 0.981 0.977 0.994 0.990 0.995 0.979 0.994 0.982 0.995 0.990 0.976 0.976 0.984 0.988 - - Overall
Specificity
= 0.983


Table 6: Confusion matrix for Gene Quiz - Yeast
Prd ⇒
Obs ⇓		 Predicted as
Energy metabolism		 Predicted as
Replication		 Predicted as
Translation		 Predicted as
Regulatory functions		 Predicted as
Cellular processes		 Predicted as
Central intermediary metabolism		 Predicted as
Transcription		 Predicted as
Cell envelope		 Predicted as
Other categories		 Predicted as
Biosynthesis of cofactors		 Predicted as
Purines		 Predicted as
Transport and binding proteins		 Predicted as
Amino acid biosynthesis		 Predicted as
Fatty acid and phospholipid metabolism		 No Prediction Row Sum Recall
Energy metabolism
in training set		 201 0 0 1 0 2 1 1 0 2 9 0 4 0 0 221 0.910
Replication
in training set		 1 110 1 20 5 3 18 3 4 4 16 0 2 4 9 200 0.550
Translation
in training set		 0 2 205 1 2 3 0 3 0 1 4 0 0 1 9 231 0.887
Regulatory functions
in training set		 2 14 7 197 10 1 14 3 5 1 26 0 0 1 9 290 0.679
Cellular processes
in training set		 8 12 3 0 283 4 6 10 3 2 2 13 1 5 5 357 0.793
Central intermediary metabolism
in training set		 4 1 5 2 6 118 0 4 0 0 4 1 8 2 3 158 0.747
Transcription
in training set		 3 14 4 15 17 5 154 2 15 1 5 3 1 0 2 241 0.639
Cell envelope
in training set		 1 4 1 2 4 4 3 56 0 0 0 10 0 0 4 89 0.629
Other categories
in training set		 0 2 0 1 3 0 7 1 25 0 0 2 0 0 3 44 0.568
Biosynthesis of cofactors
in training set		 4 1 2 0 0 2 0 0 0 33 2 1 3 0 0 48 0.688
Purines
in training set		 2 5 3 2 10 4 0 2 0 2 170 5 4 1 2 212 0.802
Transport and binding proteins
in training set		 1 1 0 2 9 11 1 28 1 0 4 221 0 1 11 291 0.759
Amino acid biosynthesis
in training set		 4 0 1 0 0 3 0 0 0 3 6 1 76 1 0 95 0.800
Fatty acid and phospholipid metabolism
in training set		 1 1 1 1 0 1 1 0 0 2 1 0 2 49 2 62 0.790
Col Sum 232 167 233 244 349 161 205 113 53 51 249 257 101 65 59 2539 Overall
Recall
= 0.748
Precision 0.866 0.659 0.880 0.807 0.811 0.733 0.751 0.496 0.472 0.647 0.683 0.860 0.752 0.754 Sequence
Coverage
= 0.977		 - Overall
Precision
= 0.765
Specificity 0.987 0.976 0.988 0.979 0.970 0.982 0.978 0.977 0.989 0.993 0.966 0.984 0.990 0.994 - - Overall
Specificity
= 0.980