Experiments of 5-fold Cross-Validation on five kingdoms

*For ontology and other abbreviations, see here

Table 1: Confusion matrix for Animal group

Prd ⇒
Obs ⇓
nuclear  mitochondrial  cytoplasmic  extracellular  golgi  peroxisomal  endoplasmic reticulum  lysosomal  membrane  No Prediction  rowSUM  recall 
nuclear 2575 2 100
11 2
0 3
0 28 125
2846 .905
mitochondrial 2 1162 18 4
0 3 2
0 2
5
1198 .970
cytoplasmic 47
16 1695 29
18 5 4
2 12 17
1845 .919
extracellular 2 0 23 3655
1 0 4 15 150 93
3943
.927
golgi 1 0 5 2
149 0 4 1 4
1
167 .892
peroxisomal 0 2 0 0 0 100 0 0 1 0
103 .971
endoplasmic reticulum 0 1 4
1
10 0 435 0 4 2
457 .952
lysosomal 0 0
4 0
0 0 0 161 4 1
170 .947
membrane 2 11 109 59
26 2 49
8
4519 35
4820 .938
colSUM 2629 1194 1958 3761
206 110 501 187 4724 279
15549 Overall Recall = .929
precision .979 .973 .866 .972 .723 .909 .868 .861 .957 Sequence Coverage = .982
  Overall Precision = .946
specificity
.996
.998
.981
.991
.996
.999
.996
.998
.981


Overall Specificity= .988

Table 2: Confusion matrix for Plant group

Prd ⇒
Obs ⇓
nuclear  mitochondrial  cytoplasmic  extracellular  golgi  mitochondrial  peroxisomal  endoplasmic reticulum  vacuolar  membrane  No Prediction  rowSUM   recall 
nuclear 162 0 1
0
1 0 0 1 0 0 3
168 .964
mitochondrial 0
287 6
1 0 10 1 0 0 0 2
307 .935
cytoplasmic 1 4 429 2 0 8
0 0 1 0 2
447 .960
extracellular 0 0 2
110 0 0 0 0 3
0
12
127 .866
golgi 0 0 0
0 34 0 0 0 0 0 1
35 .971
mitochondrial 1 18 24 1
0
1821 1 2 1
18
12
1899 .959
peroxisomal 0 0
0 0 0 1
28 0 0 0 0
29 .966
endoplasmic reticulum 0 0 1
0 0 0 0 56 3 3 1
64 .875
vacuolar 0 0 0
8
2 0 0 1
67 3
1
82 .817
membrane 0 1
2 2
3 18
0 2
2
99
6
135 .733
colSUM 164 310
465 124 40 1858 30 62 77 123 40
3293 Overall Recall = .939
precision .988 .926 .923 .887 .850 .980 .933 .903 .870 .805 Sequence Coverage = .988
  Overall Precision =  .951
specificity
.999
.992
.987
.996
.998
.973
.999
.998
.997
.992


Overall Specificity = .982

Table: Confusion matrix for Fungi Group
 
Prd ⇒
Obs ⇓
nuclear  mitochondrial  cytoplasmic  extracellular  golgi  peroxisomal  endoplasmic reticulum  membrane  vacuolar  No Prediction  rowSUM   recall 
nuclear 517 4 28
2 1 1 0
2 0 66
621 .833
mitochondrial 8 302 39
2
0 6
1 5 0 43
406 .744
cytoplasmic 23 24 319 3 3 6
3 2
3
9
395 .808
extracellular 0 3
4
149 1 1
1 2 2
8
171 .871
golgi 0
0 3
0 42 0 2
1 0
4
52 .808
peroxisomal 0
6 2
0 0 55 0 0 0 1
64 .859
endoplasmic reticulum 2 0 2
1 6
0 42 7 0 4
64 .656
membrane 4
1 7 4 6
1 6
260 3
10
302 .861
vacuolar 0 0 2 2 2 0 1 0 12 0
19 .632
colSUM 554 340 406
163 61 70 56 279 20
145
2094  Overall Recall = .811
precision .933 .888 .786 .914 .689 .786 .750 .932 .600 Sequence Coverage= .931
  Overall Precision = .871
specificity
.975
.977
.949
.993
.991
.993
.993
.989
.996


Overall Specificity = .975

Table: Confusion matrix for Gram-positive Bacteria group

Prd ⇒
Obs ⇓
cytoplasmic  cell wall  extracellular  membrane  No Prediction  rowSUM  recall 
cytoplasmic 882 1
25
13 9
930 .948
cell wall
1
15 0
1
2
19
.789
extracellular 2
2
222 8
18
252 .881
membrane 8 2
17
290 23
340 .853
colSUM 893
20 264
312 52
1541  Overall Recall = .914
precision .988 .750 .841 .929 Sequence Coverage = .966
  Overall Precision = .946
specificity
.982
.997
.967
.982


Overall Specificity = .980

Table: Confusion matrix for Gram-negative Bacteria group
 
Prd ⇒
Obs ⇓
cytoplasmic  extracellular  periplasmic  inner membrane  cell wall  outer membrane  No Prediction  rowSUM   recall 
cytoplasmic 1778 21
26 12 0 4 20
1861 .955
extracellular 3 217 6
0 2 1
24
253 .858
periplasmic 6 15
336 4 0 6 18
385
.873
inner membrane 5 1 4 411 0 0 11
432 .951
cell wall
0 1
0 0 43 1 1
46 .935
outer membrane 0 4
2 2 0 181 8
197 .919
colSUM 1792 259
374 429 45 193 82
3174  Overall Recall = .934
precision .992 .838 .898 .958 .956 .938 Sequence Coverage = .974
  Overall Precision = .959
specificity
.989
.986
.986
.993
.999
.996


Overall Specificity = .990

Table: Confusion matrix for Archea group

Prd ⇒
Obs ⇓
cytoplasmic  membrane  cell wall  extracellular No Prediction  rowSUM   recall 
cytoplasmic 401 1
0 1 1
404 .993
membrane 1 60 6
0 1
62 .968
cell wall 0 0 6 0 0 6 1.000
extracellular 0 0 0 2 3 6 .400
colSUM 402 61 6 3 5 478  Overall Recall = .983
precision .998 .984 1.000 0.667 Sequence Coverage = .990
  Overall Precision = .994
specificity
.986 .998 1.000 .998

Overall Specificity = .988