Supplemental material

Title : Biomarker selection and sample prediction in multi-stage disease on MALDI-TOF data

1. BW ratios for all 23,846 peaks : BW ratio

2. Pseudo code

3. Our source code is available.

NOTE : In order to connect weka library with libsvm, please refer to http://www.cs.waikato.ac.nz/ml/weka/ and http://www.csie.ntu.edu.tw/~cjlin/libsvm/.

4. Based on peaks found in Cirrhosis VS HCC (See Fig. 2 (a) in the paper), experiments were performed with the top one, then the top two and so forth up to the top 20 peaks using linear SVM in 10CV. With the top 10 peaks, the best accuracy was obtained.

           

For the top 10 peaks in Fig. 2 (a), ROC curve was shown.

           

5. Frequency ranking for 300 peaks in all pair of classes

Cirrhosis vs Health  Cirrhosis vs HCC Health vs HCC
Ranking Frequency m/z Ranking Frequency m/z Ranking Frequency m/z
1 195 1326.4894 1 199 1865.4808 1 144 3201.7317
2 178 1961.9057 2 189 1797.0038 2 135 3202.0519
3 177 2307.1390 3 188 2390.0313 3 128 2373.1230
4 177 1961.7096 4 182 1865.6674 4 120 2389.7923
5 173 2372.1740 5 181 2365.5415 5 119 2535.5320
6 169 1327.1527 6 181 2391.4656 6 116 2536.0392
7 158 2362.9410 7 180 1961.7096 7 113 2373.3603
8 157 2389.5533 8 179 2365.3050 8 110 3202.3721
9 147 1327.2855 9 177 2390.9874 9 105 2535.0250
10 140 1325.5612 10 172 1710.3930 10 105 2535.7856
11 140 1325.6938 11 166 2390.2703 11 102 2372.1740
12 138 1451.1138 12 162 2390.5093 12 102 1452.5656
13 138 2306.6776 13 162 2373.3603 13 101 2535.2785
14 137 1796.6444 14 160 2365.0685 14 99 3260.8598
15 136 1796.8241 15 157 2373.5976 15 98 2372.4112
16 132 2389.7923 16 152 2363.6499 16 98 2536.2928
17 129 1962.1019 17 147 2390.7483 17 95 2534.0112
18 122 1957.5945 18 146 1796.8241 18 94 3216.1712
19 119 2389.3144 19 145 2365.7780 19 89 2373.5976
20 116 1718.7941 20 144 1961.9057 20 88 5900.6426
21 113 1331.2731 21 144 2373.8350 21 87 2390.0313
22 106 1797.0038 22 135 2373.1230 22 78 1342.3681
23 96 2366.0146 23 131 2364.8320 23 76 2534.7715
24 95 2363.1773 24 125 1962.1019 24 74 1452.4203
25 93 1328.2148 25 125 1957.3988 25 73 2375.7347
26 92 2305.9857 26 124 2389.7923 26 71 1329.5437
27 91 2536.5464 27 110 1796.6444 27 71 2372.6484
28 91 1466.1367 28 108 2534.0112 28 68 1451.1138
29 87 1331.6725 29 103 3260.8598 29 67 2372.8857
30 84 1331.1400 30 102 3216.1712 30 65 1331.0069
31 83 2390.0313 31 98 1330.8738 31 63 2534.5181
32 80 1331.4062 32 96 2374.0724 32 62 1342.5023
33 79 1710.3930 33 95 1957.5945 33 62 1452.2751
34 79 2536.0392 34 93 2534.5181 34 58 2536.5464
35 74 2305.7552 35 92 2389.3144 35 56 1329.2778
36 74 2363.6499 36 92 1342.5023 36 56 2389.3144
37 72 1325.0311 37 91 2375.7347 37 53 1961.7096
38 72 2363.4136 38 91 2362.9410 38 52 2375.4972
39 69 1331.0069 39 90 1866.2271 39 51 2374.7847
40 66 2372.4112 40 88 2374.3098 40 49 2375.2596
41 64 5918.3702 41 88 2389.5533 41 48 5901.2326
42 63 5900.0526 42 86 1331.0069 42 47 2375.0221
43 63 2391.4656 43 82 2363.4136 43 47 2389.5533
44 59 1866.9737 44 77 2372.1740 44 46 2365.3050
45 58 1328.3477 45 75 2366.0146 45 46 2365.0685
46 57 5917.7784 46 70 5918.3702 46 42 1340.6242
47 56 1957.3988 47 68 2374.5472 47 41 2366.0146
48 52 5895.3346 48 66 1451.2589 48 41 1796.6444
49 48 1327.5509 49 61 2372.8857 49 39 2363.6499
50 48 1328.0820 50 58 2372.4112 50 37 2390.2703
51 47 2536.2928 51 56 2374.7847 51 36 3201.4116
52 47 5899.4626 52 54 2363.1773 52 35 1331.1400
53 43 1329.2778 53 53 2535.2785 53 34 2365.5415
54 39 5898.8727 54 50 3202.3721 54 34 1329.6766
55 39 2306.2163 55 49 1452.5656 55 33 2364.8320
56 34 1331.5394 56 48 1451.1138 56 32 2374.5472
57 34 1466.2834 57 42 2375.0221 57 31 1330.8738
58 33 3265.7545 58 41 1866.4137 58 31 2365.7780
59 31 2306.4469 59 41 1866.7870 59 28 1796.8241
60 31 1325.1636 60 39 1326.4894 60 26 1331.2731
61 28 5900.6426 61 39 2372.6484 61 25 1331.4062
62 27 1451.2589 62 34 1452.4203 62 25 1329.4107
63 26 1327.4182 63 34 1866.6004 63 24 5917.7784
64 21 1151.1287 64 33 3202.6923 64 23 2390.7483
65 20 2534.0112 65 32 1866.9737 65 18 1452.1299
66 18 2374.0724 66 31 1325.6938 66 18 5918.3702
67 18 1330.3416 67 29 2535.7856 67 15 2374.0724
68 17 1327.6837 68 26 3203.0126 68 15 2373.8350
69 17 1341.5630 69 24 1342.3681 69 14 1451.9847
70 17 5907.1365 70 23 3263.4694 70 13 3202.6923
71 13 1127.2083 71 21 1331.1400 71 10 1330.7407
72 12 2372.6484 72 21 1328.3477 72 10 5901.8228
73 12 5897.1034 73 21 2534.7715 73 9 1331.5394
74 11 1124.2815 74 21 2307.1390 74 8 2390.5093
75 11 1125.8565 75 18 1325.1636 75 7 2307.1390
76 10 2390.2703 76 18 1327.6837 76 6 2390.9874
77 10 1127.0956 77 17 1325.2961 77 6 5900.0526
78 10 5903.0032 78 17 1452.2751 78 5 1451.8395
79 10 1123.4948 79 16 1341.5630 79 5 2374.3098
80 10 2390.9874 80 14 2536.0392 80 5 1341.5630
81 10 3194.6960 81 14 1711.9330 81 4 1961.9057
82 9 1124.9562 82 13 2375.4972 82 4 3203.9736
83 9 1330.4746 83 13 1341.1606 83 3 2391.4656
84 8 2535.7856 84 13 3252.3930 84 3 1451.2589
85 8 1865.4808 85 12 1331.2731 85 3 3203.0126
86 7 3265.1015 86 12 3201.4116 86 3 3203.6532
87 7 5907.7272 87 10 3203.6532 87 3 1797.0038
88 6 1711.9330 88 9 3252.7183 88 2 1330.2086
89 5 2374.3098 89 9 3263.1431 89 2 5907.7272
90 5 2375.2596 90 9 1328.2148 90 1 2363.4136
91 4 1325.2961 91 8 1330.7407 91 1 2362.9410
92 4 3264.7750 92 8 1328.0820 92 1 1451.5492
93 4 1330.8738 93 8 1341.4288 93 1 3252.3930
94 4 1125.7439 94 7 1330.4746 94 1 5895.3346
95 4 1126.6448 95 7 1330.6077 95 1 1137.0573
96 4 1329.5437 96 7 1325.5612 96 1 1136.9436
97 4 1341.4288 97 7 1452.1299 97 1 1136.8299
98 4 1329.4107 98 7 2375.2596 98 1 1137.1710
99 3 1866.7870 99 6 3255.3213 99 1 1136.7162
100 3 1342.5023 100 6 3202.0519 100 0 3263.4694
101 3 2390.7483 101 6 3203.3329 101 0 3263.7958
102 3 5895.9242 102 6 1329.5437 102 0 3263.1431
103 3 1137.1710 103 6 1711.7618 103 0 3264.1221
104 2 2375.0221 104 6 2535.0250 104 0 1328.2148
105 2 3264.4486 105 6 5907.7272 105 0 3254.9958
106 2 1126.1943 106 6 1329.2778 106 0 3192.4606
107 2 1137.3984 107 4 1711.5906 107 0 3192.7798
108 2 1126.7575 108 4 2535.5320 108 0 3262.8168
109 2 5902.4129 109 4 5917.7784 109 0 3192.1414
110 2 1124.3939 110 3 2536.5464 110 0 1126.4195
111 1 1329.6766 111 3 3262.8168 111 0 1124.9562
112 1 5898.2829 112 3 3191.8222 112 0 3191.8222
113 1 3265.4280 113 3 3262.4906 113 0 1125.0687
114 1 1123.6072 114 3 3191.5031 114 0 1136.6026
115 1 3194.3766 115 3 1330.3416 115 0 3193.0991
116 1 1137.5122 116 3 1331.4062 116 0 5905.3647
117 1 2535.5320 117 3 3191.1839 117 0 3264.4486
118 1 3260.8598 118 2 1325.4287 118 0 3255.3213
119 1 1865.6674 119 2 3190.8649 119 0 1325.2961
120 1 1466.4300 120 2 1124.8437 120 0 3262.4906
121 1 1137.0573 121 2 1331.5394 121 0 5905.9553
122 1 1136.9436 122 2 1329.6766 122 0 1136.4889
123 1 1136.8299 123 2 1329.4107 123 0 1330.4746
124 1 1136.7162 124 2 1451.9847 124 0 1137.2847
125 1 3263.4694 125 2 1451.8395 125 0 1126.5322
126 1 3263.7958 126 2 1341.2947 126 0 3191.5031
127 0 2373.8350 127 2 1340.6242 127 0 1325.1636
128 0 3263.1431 128 2 2536.2928 128 0 1126.3069
129 0 2374.5472 129 2 1451.5492 129 0 1125.8565
130 0 2374.7847 130 2 3187.9945 130 0 1330.3416
131 0 3264.1221 131 2 3260.5338 131 0 3262.1644
132 0 3254.9958 132 2 3257.9265 132 0 3264.7750
133 0 3192.4606 133 1 1137.0573 133 0 1125.1812
134 0 3192.7798 134 1 1136.9436 134 0 5906.5459
135 0 3262.8168 135 1 1136.8299 135 0 3193.4184
136 0 3192.1414 136 1 1137.1710 136 0 1330.6077
137 0 2373.5976 137 1 1136.7162 137 0 1125.9691
138 0 1126.4195 138 1 3263.7958 138 0 1125.7439
139 0 3191.8222 139 1 3264.1221 139 0 1327.2855
140 0 1125.0687 140 1 3254.9958 140 0 3191.1839
141 0 1136.6026 141 1 3192.4606 141 0 1125.5188
142 0 3193.0991 142 1 3192.7798 142 0 1126.9829
143 0 5905.3647 143 1 3192.1414 143 0 1327.4182
144 0 3255.3213 144 0 1126.4195 144 0 5904.7743
145 0 3262.4906 145 0 1124.9562 145 0 3249.4673
146 0 5905.9553 146 0 1125.0687 146 0 3255.6469
147 0 1136.4889 147 0 1136.6026 147 0 3254.6704
148 0 1137.2847 148 0 3193.0991 148 0 1125.4063
149 0 3202.6923 149 0 5905.3647 149 0 1325.4287
150 0 1126.5322 150 0 3264.4486 150 0 1126.1943
151 0 3191.5031 151 0 5905.9553 151 0 3190.5458
152 0 1126.3069 152 0 1136.4889 152 0 3190.8649
153 0 2375.4972 153 0 1137.2847 153 0 1125.2937
154 0 3262.1644 154 0 1126.5322 154 0 3256.2980
155 0 3202.3721 155 0 1126.3069 155 0 1125.6314
156 0 3203.0126 156 0 1125.8565 156 0 1328.3477
157 0 1125.1812 157 0 3262.1644 157 0 3255.9724
158 0 5906.5459 158 0 3264.7750 158 0 3203.3329
159 0 2373.3603 159 0 1125.1812 159 0 3261.8382
160 0 3193.4184 160 0 5906.5459 160 0 5899.4626
161 0 1330.6077 161 0 3193.4184 161 0 3188.9510
162 0 1125.9691 162 0 1125.9691 162 0 1126.8702
163 0 2365.5415 163 0 1125.7439 163 0 1126.6448
164 0 3202.0519 164 0 1327.2855 164 0 3190.2268
165 0 1330.7407 165 0 1125.5188 165 0 3189.2699
166 0 3191.1839 166 0 1126.9829 166 0 1124.8437
167 0 1125.5188 167 0 1327.4182 167 0 3193.7378
168 0 1126.9829 168 0 5904.7743 168 0 3189.9078
169 0 5904.7743 169 0 3249.4673 169 0 1154.9335
170 0 3249.4673 170 0 3255.6469 170 0 1154.1254
171 0 3255.6469 171 0 3254.6704 171 0 3265.1015
172 0 3254.6704 172 0 1125.4063 172 0 1126.0817
173 0 1125.4063 173 0 1126.1943 173 0 1137.3984
174 0 1325.4287 174 0 3190.5458 174 0 5904.1838
175 0 3190.5458 175 0 1125.2937 175 0 1154.8181
176 0 3190.8649 176 0 3256.2980 176 0 1126.7575
177 0 1125.2937 177 0 1125.6314 177 0 1153.6639
178 0 3256.2980 178 0 3255.9724 178 0 3189.5888
179 0 1125.6314 179 0 3261.8382 179 0 3249.1424
180 0 3255.9724 180 0 5899.4626 180 0 1328.0820
181 0 3203.3329 181 0 3188.9510 181 0 3256.6237
182 0 3261.8382 182 0 1126.8702 182 0 1153.7792
183 0 2365.3050 183 0 1126.6448 183 0 1136.3753
184 0 3188.9510 184 0 3190.2268 184 0 1327.5509
185 0 1126.8702 185 0 3201.7317 185 0 5903.5935
186 0 2375.7347 186 0 3189.2699 186 0 1150.8985
187 0 3190.2268 187 0 3193.7378 187 0 3261.5120
188 0 3201.7317 188 0 3189.9078 188 0 5902.4129
189 0 3189.2699 189 0 1154.9335 189 0 1127.0956
190 0 1124.8437 190 0 1154.1254 190 0 1325.5612
191 0 3193.7378 191 0 3265.1015 191 0 1711.7618
192 0 3189.9078 192 0 1126.0817 192 0 5907.1365
193 0 2365.0685 193 0 1137.3984 193 0 1154.0100
194 0 1154.9335 194 0 5904.1838 194 0 1341.1606
195 0 1154.1254 195 0 1154.8181 195 0 3194.0572
196 0 1126.0817 196 0 1126.7575 196 0 3188.6321
197 0 5904.1838 197 0 1153.6639 197 0 5903.0032
198 0 1154.8181 198 0 3189.5888 198 0 1155.0490
199 0 1153.6639 199 0 3249.1424 199 0 3250.7673
200 0 3189.5888 200 0 5900.0526 200 0 1151.0136
201 0 3249.1424 201 0 3256.6237 201 0 1341.0265
202 0 2365.7780 202 0 1153.7792 202 0 1154.2408
203 0 3256.6237 203 0 1136.3753 203 0 1327.6837
204 0 1153.7792 204 0 5901.8228 204 0 1150.7835
205 0 1136.3753 205 0 1327.5509 205 0 1154.7026
206 0 5901.8228 206 0 5903.5935 206 0 2306.2163
207 0 5903.5935 207 0 1150.8985 207 0 1124.3939
208 0 3201.4116 208 0 3261.5120 208 0 3254.3449
209 0 1150.8985 209 0 5902.4129 209 0 5898.8727
210 0 3261.5120 210 0 1127.0956 210 0 3250.1173
211 0 1711.7618 211 0 5907.1365 211 0 3251.0924
212 0 1154.0100 212 0 1154.0100 212 0 1124.7313
213 0 1341.1606 213 0 3194.0572 213 0 1325.6938
214 0 3194.0572 214 0 3188.6321 214 0 2305.9857
215 0 2373.1230 215 0 5903.0032 215 0 3250.4423
216 0 3188.6321 216 0 1155.0490 216 0 1124.5064
217 0 1155.0490 217 0 3250.7673 217 0 1153.5485
218 0 3250.7673 218 0 1151.0136 218 0 5898.2829
219 0 1151.0136 219 0 1341.0265 219 0 1340.8924
220 0 1341.0265 220 0 5901.2326 220 0 3261.1859
221 0 5901.2326 221 0 1154.2408 221 0 3265.4280
222 0 1154.2408 222 0 1150.7835 222 0 1123.4948
223 0 1150.7835 223 0 5900.6426 223 0 1340.7583
224 0 1154.7026 224 0 1154.7026 224 0 1136.1480
225 0 3254.3449 225 0 2306.2163 225 0 1341.4288
226 0 2364.8320 226 0 1124.3939 226 0 1152.1652
227 0 3250.1173 227 0 3254.3449 227 0 1150.6684
228 0 3251.0924 228 0 5898.8727 228 0 1153.8946
229 0 3203.6532 229 0 3250.1173 229 0 1152.5108
230 0 1124.7313 230 0 3251.0924 230 0 1123.6072
231 0 1330.2086 231 0 1124.7313 231 0 3194.3766
232 0 3250.4423 232 0 1330.2086 232 0 3249.7923
233 0 1124.5064 233 0 2305.9857 233 0 5897.6931
234 0 1153.5485 234 0 3250.4423 234 0 1152.2804
235 0 1340.8924 235 0 1124.5064 235 0 1957.5945
236 0 3261.1859 236 0 1153.5485 236 0 1124.6188
237 0 1340.7583 237 0 5898.2829 237 0 2306.4469
238 0 1136.1480 238 0 1340.8924 238 0 3188.3133
239 0 1152.1652 239 0 3261.1859 239 0 1152.3956
240 0 1150.6684 240 0 3265.4280 240 0 1154.5871
241 0 1153.8946 241 0 1123.4948 241 0 1711.5906
242 0 1152.5108 242 0 1340.7583 242 0 1127.2083
243 0 3249.7923 243 0 1136.1480 243 0 1153.4332
244 0 5897.6931 244 0 1152.1652 244 0 1866.6004
245 0 1451.9847 245 0 1150.6684 245 0 1123.7195
246 0 2535.0250 246 0 1153.8946 246 0 1341.2947
247 0 1152.2804 247 0 1152.5108 247 0 1331.6725
248 0 1451.8395 248 0 1123.6072 248 0 1137.5122
249 0 2535.2785 249 0 3194.3766 249 0 1152.6261
250 0 1124.6188 250 0 3249.7923 250 0 3256.9493
251 0 1452.1299 251 0 5897.6931 251 0 1154.3563
252 0 3188.3133 252 0 1152.2804 252 0 1327.1527
253 0 2534.7715 253 0 1124.6188 253 0 1711.9330
254 0 1152.3956 254 0 2306.4469 254 0 1962.1019
255 0 1154.5871 255 0 3188.3133 255 0 1451.6943
256 0 2372.8857 256 0 1152.3956 256 0 1154.4717
257 0 1711.5906 257 0 1154.5871 257 0 3257.2750
258 0 1153.4332 258 0 1127.2083 258 0 1136.0344
259 0 1866.6004 259 0 1153.4332 259 0 3248.8175
260 0 1123.7195 260 0 1123.7195 260 0 1151.1287
261 0 1341.2947 261 0 1331.6725 261 0 2363.1773
262 0 2390.5093 262 0 1137.5122 262 0 1136.2617
263 0 1152.6261 263 0 1152.6261 263 0 5897.1034
264 0 1340.6242 264 0 3256.9493 264 0 1866.4137
265 0 3256.9493 265 0 1154.3563 265 0 2534.2646
266 0 1154.3563 266 0 1327.1527 266 0 1866.7870
267 0 1452.2751 267 0 1451.6943 267 0 3257.6008
268 0 1451.6943 268 0 1154.4717 268 0 1466.2834
269 0 1154.4717 269 0 3257.2750 269 0 1710.3930
270 0 3257.2750 270 0 1136.0344 270 0 3258.5781
271 0 1136.0344 271 0 3248.8175 271 0 3251.4175
272 0 3248.8175 272 0 1151.1287 272 0 1152.0500
273 0 1136.2617 273 0 1136.2617 273 0 1325.0311
274 0 2534.5181 274 0 5897.1034 274 0 3258.9040
275 0 1866.4137 275 0 2534.2646 275 0 2305.7552
276 0 2534.2646 276 0 3257.6008 276 0 1466.1367
277 0 3257.6008 277 0 1466.2834 277 0 3187.9945
278 0 1452.4203 278 0 3258.5781 278 0 1865.6674
279 0 3258.5781 279 0 3251.4175 279 0 1451.4040
280 0 3251.4175 280 0 1152.0500 280 0 1957.3988
281 0 1152.0500 281 0 1325.0311 281 0 1124.2815
282 0 3258.9040 282 0 3258.9040 282 0 1466.4300
283 0 3203.9736 283 0 2305.7552 283 0 1152.7414
284 0 1451.5492 284 0 3203.9736 284 0 3259.5558
285 0 3187.9945 285 0 1466.1367 285 0 1152.8566
286 0 1451.4040 286 0 1451.4040 286 0 1865.4808
287 0 3252.3930 287 0 1124.2815 287 0 3265.7545
288 0 1342.3681 288 0 1466.4300 288 0 3259.8818
289 0 1152.7414 289 0 1152.7414 289 0 1866.9737
290 0 3259.5558 290 0 3259.5558 290 0 2306.6776
291 0 1152.8566 291 0 1152.8566 291 0 3260.5338
292 0 1452.5656 292 0 5895.3346 292 0 1866.2271
293 0 3259.8818 293 0 3265.7545 293 0 3194.6960
294 0 3216.1712 294 0 3259.8818 294 0 3257.9265
295 0 3260.5338 295 0 2306.6776 295 0 1326.4894
296 0 1866.2271 296 0 3194.6960 296 0 3258.2523
297 0 3257.9265 297 0 3258.2523 297 0 3252.7183
298 0 3258.2523 298 0 1718.7941 298 0 1718.7941
299 0 3252.7183 299 0 1152.9719 299 0 1152.9719
300 0 1152.9719 300 0 5895.9242 300 0 5895.9242