Performance of PHENOTYPE, GO ENRICHMENT, and KNOWN GENES methods in the benchmark
Performance of PHENOTYPE, GO ENRICHMENT, and KNOWN GENES methods in the benchmark G2D Home

In order to benchmark the performance of the algorithms, 227 OMIM phenotypes that were linked to more than one gene (i.e.mutations in different genes that produce the same phenotype) were selected from the EntrezGene database.

For each disease, we fixed one gene as the "target gene". Then, to do the predictions, we defined a chromosomal region of 30 Mb around the target gene. All the tested methods use different inputs but the predictions were made in the same bands around the target genes.

DISEASE PHENOTYPE GO ENRICHMENT KNOWN GENES
OMIM TARGET GENE GENES IN TARGET BAND position relative position relative position relative
101400 2263 214 14 6.07% 102 47.20% 96 44.39%
102200 2778 460 16 3.26% 42 8.91% 9 1.74%
103470 4286 82 6 6.10% 8 8.54% 6 6.10%
103780 2555 102 7 5.88% 15 13.73% 1 0.00%
104300 323 90 21 22.22% 26 27.78% 35 37.78%
105150 19 215 25 11.16% 75 34.42% 69 31.63%
105200 2243 117 9 6.84% 32 26.50% 17 13.68%
105400 1639 234 138 58.55% 38 15.81% 120 50.85%
105830 4204 251 64 25.10% 71 27.89% 53 20.72%
107250 2301 364 60 16.21% 191 52.20% 12 3.02%
109800 2261 189 110 57.67% 69 35.98% 56 29.10%
111400 8706 145 50 33.79% 13 8.28% 5 2.76%
113800 3848 396 3 0.51% 1 0.00% 4 0.76%
114030 4292 343 78 22.45% 86 24.78% 174 50.44%
114480 472 238 131 54.62% 99 41.18% 102 42.44%
114500 701 256 44 16.80% 61 23.44% 103 39.84%
114550 841 181 105 57.46% 120 65.75% 91 49.72%
115200 70 252 73 28.57% 73 28.57% 50 19.44%
120200 5080 177 96 53.67% 47 25.99% 105 58.76%
122000 1296 471 112 23.57% 274 57.96% 202 42.68%
122100 3850 396 25 6.06% 132 33.08% 20 4.80%
122700 1548 828 553 66.67% 352 42.39% 512 61.71%
123150 2260 181 9 4.42% 9 4.42% 9 4.42%
123700 2006 168 1 0.00% 15 8.33% 9 4.76%
124000 617 238 19 7.56% 141 58.82% 1 0.00%
125850 3172 439 41 9.11% 155 35.08% 262 59.45%
125853 208 802 450 55.99% 436 54.24% 257 31.92%
126200 4261 467 77 16.27% 90 19.06% 258 55.03%
127750 6620 238 113 47.06% 160 66.81% 148 61.76%
130000 1277 608 345 56.58% 417 68.42% 300 49.18%
130020 1281 188 2 0.53% 6 2.66% 3 1.06%
130060 1277 608 5 0.66% 1 0.00% 1 0.00%
130650 1028 389 70 17.74% 80 20.31% 253 64.78%
131800 3691 421 39 9.03% 77 18.05% 51 11.88%
132600 1499 385 216 55.84% 72 18.44% 222 57.40%
133200 2707 482 156 32.16% 305 63.07% 294 60.79%
133239 6049 137 62 44.53% 84 60.58% 76 54.74%
133780 4041 586 280 47.61% 346 58.87% 285 48.46%
136880 5959 427 152 35.36% 217 50.59% 290 67.68%
137215 324 80 25 30.00% 23 27.50% 5 5.00%
137750 1545 227 42 18.06% 60 25.99% 135 59.03%
137760 1545 227 42 18.06% 122 53.30% 90 39.21%
137800 1755 214 83 38.32% 81 37.38% 81 37.38%
142623 1908 460 148 31.96% 204 44.13% 201 43.48%
143465 1816 189 1 0.00% 33 16.93% 12 5.82%
143890 19 215 35 15.81% 89 40.93% 73 33.49%
144200 3857 605 25 3.97% 313 51.57% 22 3.47%
144700 4968 184 80 42.93% 50 26.63% NA 0.00%
145000 4221 580 338 58.10% 176 30.17% NA 0.00%
145500 118 189 88 46.03% 111 58.20% 112 58.73%
145750 6101 135 38 27.41% 65 47.41% 50 36.30%
145900 1959 213 69 31.92% 28 12.68% 7 2.82%
146110 26012 428 62 14.25% 252 58.64% 161 37.38%
146200 846 251 5 1.59% 27 10.36% 6 1.99%
147050 2206 615 234 37.89% 205 33.17% 347 56.26%
148700 1828 135 6 3.70% 41 29.63% 11 7.41%
149400 2741 346 60 17.05% 21 5.78% 6 1.45%
151400 595 586 324 55.12% 158 26.79% 367 62.46%
151623 1029 186 4 1.61% 11 5.38% 9 4.30%
151660 4000 556 48 8.45% 118 21.04% 233 41.73%
152700 356 323 121 37.15% 92 28.17% 106 32.51%
155240 4914 566 30 5.12% 384 67.67% 103 18.02%
155255 29 494 310 62.55% 208 41.90% 160 32.19%
157300 1909 106 21 18.87% 29 26.42% 31 28.30%
157640 291 99 1 0.00% 28 27.27% 4 3.03%
158000 3887 394 23 5.58% 210 53.05% 23 5.58%
158350 657 302 69 22.52% 86 28.15% 32 10.26%
158810 1291 348 50 14.08% 109 31.03% 37 10.34%
159900 1813 287 54 18.47% 88 30.31% 49 16.72%
161800 58 200 24 11.50% 48 23.50% 34 16.50%
164230 627 158 96 60.13% 78 48.73% 105 65.82%
165720 1280 388 157 40.21% 220 56.44% 267 68.56%
166710 799 284 63 21.83% 139 48.59% 156 54.58%
167200 3853 394 23 5.58% 154 38.83% 24 5.84%
167210 3854 394 23 5.58% 152 38.32% 24 5.84%
167800 5644 261 2 0.38% 127 48.28% 120 45.59%
168000 6390 448 9 1.79% 3 0.45% 1 0.00%
168500 4488 238 158 65.97% 148 61.76% 161 67.23%
168600 1621 428 182 42.29% 73 16.82% 257 59.81%
170400 779 259 61 23.17% 37 13.90% 28 10.42%
171300 6392 287 36 12.20% 185 64.11% 101 34.84%
172700 4137 586 171 29.01% 162 27.47% 384 65.36%
174050 5589 668 412 61.53% 279 41.62% 274 40.87%
174900 657 302 29 9.27% 12 3.64% 1 0.00%
176200 3077 502 11 1.99% 72 14.14% 148 29.28%
176270 4692 88 28 30.68% 41 45.45% 19 20.45%
176807 367 182 2 0.55% 9 4.40% 23 12.09%
177200 6338 301 30 9.63% 66 21.59% 16 4.98%
178500 6435 257 6 1.95% 84 32.30% 36 13.62%
180300 861 348 168 47.99% 83 23.56% 153 43.68%
180800 4359 573 17 2.79% 191 33.16% 93 16.06%
180849 1387 467 11 2.14% 8 1.50% 1 0.00%
181000 3123 593 361 60.71% 312 52.45% 410 68.97%
181500 207 244 8 2.87% 33 13.11% 23 9.02%
182940 4548 254 5 1.57% 2 0.39% 1 0.00%
187500 182 277 54 19.13% 11 3.61% 19 6.50%
187950 3717 122 37 29.51% 20 15.57% 46 36.89%
188470 3265 389 240 61.44% 106 26.99% 284 72.75%
188550 5108 227 83 36.12% 142 62.11% 97 42.29%
189800 4846 244 84 34.02% 51 20.49% NA 0.00%
190685 2623 236 112 47.03% 92 38.56% 141 59.32%
191100 3458 292 166 56.51% 152 51.71% 146 49.66%
192600 70 252 97 38.10% 82 32.14% 43 16.67%
193300 595 586 190 32.25% 160 27.13% 61 10.24%
193900 3851 396 20 4.80% 132 33.08% 24 5.81%
194070 675 177 18 9.60% 41 22.60% 55 30.51%
201400 1392 132 3 1.52% 60 44.70% 78 58.33%
202370 5189 274 44 15.69% 116 41.97% 30 10.58%
202400 2243 117 3 1.71% 7 5.13% 5 3.42%
202700 1991 668 420 62.72% 309 46.11% 392 58.53%
203300 3257 294 25 8.16% 156 52.72% 127 42.86%
203450 2670 597 217 36.18% 263 43.89% 248 41.37%
203780 1285 281 47 16.37% 33 11.39% 131 46.26%
204000 1406 915 584 63.72% 322 35.08% 428 46.67%
209880 627 158 105 65.82% 68 42.41% 76 47.47%
209900 582 578 276 47.58% 268 46.19% 324 55.88%
209920 4261 467 158 33.62% 256 54.60% 277 59.10%
209950 3459 166 110 65.66% 53 31.33% 68 40.36%
210250 64240 151 47 30.46% 58 37.75% 1 0.00%
211900 2591 170 20 11.18% 10 5.29% 107 62.35%
211980 673 253 124 48.62% 104 40.71% 84 32.81%
214100 5189 274 90 32.48% 97 35.04% 46 16.42%
214150 2068 915 17 1.75% 20 2.08% 1 0.00%
215600 3856 396 66 16.41% 198 49.75% 21 5.05%
217095 6899 289 13 4.15% 71 24.22% NA 0.00%
219000 80144 204 111 53.92% 68 32.84% 13 5.88%
219050 3640 553 313 56.42% 79 14.10% 182 32.73%
219100 4015 147 1 0.00% 16 10.20% 8 4.76%
220400 3753 348 136 38.79% 117 33.33% 55 15.52%
221770 7305 618 129 20.71% 106 16.99% 20 3.07%
223100 3938 110 1 0.00% 61 54.55% 40 35.45%
224900 10913 222 1 0.00% 92 40.99% 8 3.15%
225500 2121 189 34 17.46% 87 45.50% 29 14.81%
226650 1308 300 9 2.67% 18 5.67% 7 2.00%
226700 3909 147 73 48.98% 71 47.62% 18 11.56%
226730 3655 169 78 45.56% 70 40.83% 81 47.34%
227300 3998 124 31 24.19% 56 44.35% 54 42.74%
231200 2811 494 1 0.00% 20 3.85% 1 0.00%
231680 2108 339 94 27.43% 27 7.67% 1 0.00%
236670 2218 217 125 57.14% 86 39.17% 79 35.94%
242100 242 494 216 43.52% 95 19.03% 196 39.47%
244400 1767 70 2 1.43% 1 0.00% 1 0.00%
248200 24 152 1 0.00% 26 16.45% 3 1.32%
248310 948 199 71 35.18% 44 21.61% 54 26.63%
251880 1716 234 13 5.13% 8 2.99% 6 2.14%
252010 4719 225 118 52.00% 142 62.67% 106 46.67%
252150 4337 614 187 30.29% 324 52.61% 387 62.87%
254500 595 586 265 45.05% 11 1.71% 19 3.07%
254780 7957 188 134 70.74% 41 21.28% 106 55.85%
256000 617 238 161 67.23% 159 66.39% 115 47.90%
256450 3767 302 10 2.98% 13 3.97% 8 2.32%
256700 4830 581 302 51.81% 301 51.64% 292 50.09%
258100 6011 105 34 31.43% 20 18.10% 6 4.76%
259420 1277 608 1 0.00% 1 0.00% 1 0.00%
259500 5925 133 7 4.51% 2 0.75% 1 0.00%
259700 1186 467 79 16.70% 122 25.91% 53 11.13%
260350 675 177 69 38.42% 68 37.85% 86 48.02%
261100 8029 173 1 0.00% 72 41.04% 46 26.01%
261515 30 383 3 0.52% 46 11.75% 2 0.26%
261550 268 668 1 0.00% 1 0.00% 1 0.00%
264350 6337 335 1 0.00% 4 0.90% 1 0.00%
265120 1439 528 1 0.00% 27 4.92% 1 0.00%
266500 5191 162 57 34.57% 95 58.02% 35 20.99%
266510 5189 274 28 9.85% 73 26.28% 78 28.10%
266600 9231 237 154 64.56% 146 61.18% 75 31.22%
267430 183 201 87 42.79% 70 34.33% 105 51.74%
268000 1258 309 2 0.32% 1 0.00% 4 0.97%
268220 2308 182 39 20.88% 64 34.62% 28 14.84%
275000 1493 205 119 57.56% 117 56.59% 95 45.85%
276300 324 80 17 20.00% 27 32.50% 41 50.00%
277580 1908 460 138 29.78% 83 17.83% 44 9.35%
300009 1184 237 31 12.66% 66 27.43% 58 24.05%
303700 2652 251 3 0.80% 55 21.51% 2 0.40%
310200 1756 135 18 12.59% 48 34.81% 18 12.59%
312750 4204 251 58 22.71% 150 59.36% 68 26.69%
600101 2707 482 50 10.17% 303 62.66% 294 60.79%
600263 3459 166 31 18.07% 111 66.27% 30 17.47%
600669 785 95 12 11.58% 50 51.58% 16 15.79%
600794 2617 221 53 23.53% 111 49.77% 145 65.16%
600802 915 294 28 9.18% 5 1.36% 22 7.14%
600807 240 141 1 0.00% 62 43.26% 21 14.18%
601386 491 184 26 13.59% 45 23.91% 12 5.98%
601457 5896 179 16 8.38% 78 43.02% 13 6.70%
601462 1134 169 98 57.40% 90 52.66% 51 29.59%
601544 2706 106 1 0.00% 26 23.58% 1 0.00%
601626 861 348 159 45.40% 177 50.57% 148 42.24%
601665 154 384 234 60.68% 99 25.52% 165 42.71%
601675 2068 915 562 61.31% 113 12.24% 51 5.46%
601680 7136 389 209 53.47% 115 29.31% 204 52.19%
602080 8792 120 15 11.67% 31 25.00% 34 27.50%
602089 2324 238 2 0.42% 7 2.52% 2 0.42%
602390 57817 584 197 33.56% 153 26.03% 330 56.34%
602475 1291 348 95 27.01% 189 54.02% 196 56.03%
602522 1187 474 22 4.43% 209 43.88% 91 18.99%
602722 6521 596 141 23.49% 258 43.12% 253 42.28%
603075 3075 273 139 50.55% 73 26.37% 193 70.33%
603554 5896 179 112 62.01% 98 54.19% 117 64.80%
603896 1967 319 48 14.73% 1 0.00% 2 0.31%
603932 1298 478 177 36.82% 291 60.67% 308 64.23%
604219 4284 427 134 31.15% 112 26.00% 60 13.82%
604233 2566 202 117 57.43% 143 70.30% 138 67.82%
604367 5468 184 82 44.02% 63 33.70% 24 12.50%
604370 4978 296 92 30.74% 149 50.00% 89 29.73%
604571 6891 594 214 35.86% 349 58.59% 175 29.29%
604772 845 195 28 13.85% 39 19.49% 6 2.56%
604931 3290 281 111 39.15% 77 27.05% 4 1.07%
605074 4233 183 1 0.00% 88 47.54% 77 41.53%
605253 1959 213 3 0.94% 2 0.47% 1 0.00%
605462 5727 196 104 52.55% 50 25.00% 90 45.41%
605899 275 393 183 46.31% 76 19.08% 178 45.04%
606054 5095 105 1 0.00% 53 49.52% 1 0.00%
606176 2645 181 16 8.29% 68 37.02% 114 62.43%
606657 4976 219 8 3.20% 25 10.96% 60 26.94%
606690 7248 428 144 33.41% 14 3.04% 2 0.23%
606764 3815 94 41 42.55% 4 3.19% 17 17.02%
606904 785 95 24 24.21% 59 61.05% 12 11.58%
607174 4330 479 364 75.78% 288 59.92% 307 63.88%
607208 2566 202 12 5.45% 31 14.85% 17 7.92%
607554 3784 389 6 1.29% 27 6.68% 6 1.29%
607748 570 224 4 1.34% 35 15.18% 30 12.95%
607785 4763 561 262 46.52% 231 41.00% 304 54.01%
607948 3458 292 7 2.05% 92 31.16% 33 10.96%
608161 5961 553 3 0.36% 263 47.38% 2 0.18%
608930 1134 169 98 57.40% 90 52.66% 51 29.59%
608931 1140 494 151 30.36% 86 17.21% 95 19.03%
609135 3458 292 47 15.75% 79 26.71% 44 14.73%
609192 7046 225 112 49.33% 23 9.78% 85 37.33%

Meaning of the column headers

DISEASE

Inherited disease that has been linked to mutations in more than one gene.

OMIM: MIM number of the disease.

TARGET GENE: Entrez Gene identifier of the target gene.

GENES IN TARGET: Number of genes contained in the chromosomal region of 30 Mb around the target genes where predictions were made.

PHENOTYPE

Gene scoring is based on the phenotype. The input are the MeSH C terms annotating the papers linked to the disease through OMIM. It computes a scoring system for the GO terms that it is used to sort the genes in the target band.

GO ENRICHMENT

Prioritization is based on a GO scoring system derived from the p-values of finding a particular GO term in more than one loci linked to the disease. Given a disease, the input for this method consists of all the bands of 30 Mb taken around all the genes that have been linked to the disease.

KNOWN GENES

This method measures the semantic similarity of the genes in the target band with all the rest of genes that are known to cause the same phenotype.

position: ranking of the disease causing gene (or target gene) in the list of genes in the band according to the score.

relative: position divided by the number of genes in the band.