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Human liver cohort, top 5K genes
Modules
Identical beta, module diff=1.0%
grey turquoise blue brown yellow green red black
grey 3573 0 0 0 0 0 0 0
turquoise 30 730 0 0 0 0 0 0
blue 0 0 261 0 0 0 0 0
brown 0 0 0 136 0 0 0 0
yellow 0 0 0 0 100 0 0 0
green 0 0 0 0 0 88 0 0
red 0 0 0 0 0 0 51 0
black 0 0 0 0 0 0 0 43
Comparison to published results
Module membership of P450 genes in the published Research Genetics paper:
NOT P450
grey 2005 9
turquoise 1314 47
blue 617 0
brown 451 0
yellow 192 0
green 106 0
red 75 0
black 71 0
pink 70 0
magenta 55 0
i.e. 47/56 are grouped into a single module and the remaining 6 are in no module.
Comparison of newly run Sage code to published modules:
grey turquoise brown blue green yellow red pink black magenta
grey 2006 677 259 250 106 104 71 70 48 12
turquoise 4 680 7 16 0 0 2 0 21 0
blue 4 2 2 253 0 0 0 0 0 0
brown 0 2 132 0 0 0 2 0 0 0
yellow 0 0 0 98 0 0 0 0 2 0
green 0 0 0 0 0 88 0 0 0 0
red 0 0 51 0 0 0 0 0 0 0
black 0 0 0 0 0 0 0 0 0 43
There is 39% difference. Checking the P450 genes
NOT P450
grey 3580 23
turquoise 697 33
blue 261 0
brown 136 0
yellow 100 0
green 88 0
red 51 0
black 43 0
only 33 are grouped together, the remaining ones are unclustered.
The publication says beta was set to 5.5, not 11. So we reran the Sage code with that beta:
grey blue turquoise brown yellow green red black pink magenta
grey 971 0 0 0 0 0 0 0 0 0
blue 4 617 0 0 0 0 0 0 0 0
brown 0 0 602 0 0 0 0 0 0 0
turquoise 170 0 0 439 0 0 75 0 0 0
yellow 5 0 347 0 0 0 0 0 0 0
green 0 0 272 0 0 0 0 0 0 0
red 39 0 0 0 192 0 0 0 0 0
magenta 148 0 0 0 0 0 0 0 0 0
black 126 0 0 12 0 0 0 0 70 0
pink 58 0 0 0 0 106 0 0 0 0
purple 0 0 104 0 0 0 0 0 0 0
tan 80 0 0 0 0 0 0 0 0 0
greenyellow 18 0 0 0 0 0 0 71 0 0
salmon 59 0 0 0 0 0 0 0 0 0
cyan 56 0 0 0 0 0 0 0 0 0
midnightblue 0 0 0 0 0 0 0 0 0 55
lightcyan 45 0 0 0 0 0 0 0 0 0
lightgreen 44 0 0 0 0 0 0 0 0 0
grey60 44 0 0 0 0 0 0 0 0 0
lightyellow 39 0 0 0 0 0 0 0 0 0
coral 38 0 0 0 0 0 0 0 0 0
sienna 0 0 36 0 0 0 0 0 0 0
gold 36 0 0 0 0 0 0 0 0 0
peru 34 0 0 0 0 0 0 0 0 0
and still got 18% difference in module membership. Checking the P450 genes:
NOT P450
grey 966 5
turquoise 682 2
blue 621 0
brown 591 11
yellow 349 3
green 244 28
red 231 0
black 208 0
pink 164 0
magenta 148 0
purple 101 3
greenyellow 89 0
tan 80 0
salmon 59 0
cyan 56 0
midnightblue 55 0
lightcyan 45 0
lightgreen 44 0
grey60 44 0
lightyellow 39 0
coral 38 0
sienna 34 2
peru 34 0
gold 34 2
i.e. 28 are grouped together. The rest are scattered across modules.
Methylation (full set)
Soft Threshold Choice
Cut | p-value | Adj R^2 | Truncated Adj R^2 | slope | mean(k) | median(k) | max(k) | Power | SFT.R.sq | slope | truncated.R.sq | mean.k. | median.k. | max.k. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | -1 | -0.00512 | -0.0562 | 0.247 | 2120 | 2230 | 3640 | 1 | 0.039759972 | 0.169460948 | -0.042121587 | 7249.755797 | 7583.706845 | 12508.45604 |
1.5 | -1 | 0.0167 | 0.413 | -0.215 | 1410 | 1350 | 2880 | 1.5 | 0.140389955 | -0.269553255 | 0.59303507 | 4828.992487 | 4542.145536 | 10029.03836 |
2 | -1 | 0.184 | 0.688 | -0.366 | 1020 | 845 | 2400 | 2 | 0.276562808 | -0.390168503 | 0.631322022 | 3491.738926 | 2824.215768 | 8386.544599 |
2.5 | -1 | 0.257 | 0.645 | -0.414 | 778 | 541 | 2040 | 2.5 | 0.362446542 | -0.458433391 | 0.523661313 | 2655.348672 | 1808.299631 | 7173.887246 |
3 | -1 | 0.323 | 0.563 | -0.453 | 611 | 356 | 1760 | 3 | 0.42871745 | -0.515750913 | 0.431061197 | 2086.334341 | 1176.893287 | 6223.960796 |
3.5 | -1 | 0.386 | 0.51 | -0.49 | 491 | 238 | 1540 | 3.5 | 0.46604534 | -0.560354757 | 0.369873339 | 1676.348853 | 781.2514422 | 5452.12826 |
4 | -1 | 0.451 | 0.509 | -0.516 | 401 | 160 | 1350 | 4 | 0.493523645 | -0.60630005 | 0.358279952 | 1368.885142 | 527.8374153 | 4809.805129 |
4.5 | -1 | 0.504 | 0.513 | -0.545 | 331 | 112 | 1190 | 4.5 | 0.51122219 | -0.643452727 | 0.371756376 | 1131.587843 | 368.4541959 | 4266.321824 |
5 | -1 | 0.542 | 0.521 | -0.577 | 276 | 81 | 1050 | 5 | 0.522934331 | -0.681405777 | 0.399981701 | 944.5030783 | 259.4558865 | 3800.880221 |
5.5 | -1 | 0.571 | 0.536 | -0.608 | 232 | 57.9 | 939 | 5.5 | 0.532765178 | -0.72250099 | 0.440336737 | 794.5816675 | 186.1875426 | 3398.594443 |
6 | -1 | 0.588 | 0.556 | -0.636 | 196 | 42.3 | 838 | 6 | 0.543038666 | -0.754901305 | 0.481364519 | 672.8857753 | 135.1591844 | 3048.3654 |
6.5 | -1 | 0.612 | 0.591 | -0.664 | 167 | 30.8 | 750 | 6.5 | 0.546592526 | -0.787367292 | 0.521630192 | 573.065346 | 99.6082135 | 2741.653967 |
7 | -1 | 0.635 | 0.628 | -0.688 | 143 | 23 | 673 | 7 | 0.546688103 | -0.824100826 | 0.556997344 | 490.4753338 | 72.92787987 | 2471.728523 |
7.5 | -1 | 0.634 | 0.646 | -0.724 | 123 | 17.1 | 606 | 7.5 | 0.540586249 | -0.867631489 | 0.58655908 | 421.6371568 | 54.2456294 | 2233.179306 |
8 | -1 | 0.652 | 0.682 | -0.744 | 106 | 12.7 | 547 | 8 | 0.548418618 | -0.896985225 | 0.619099353 | 363.8954176 | 40.26400042 | 2021.591247 |
8.5 | -1 | 0.646 | 0.691 | -0.776 | 91.5 | 9.69 | 494 | 8.5 | 0.564768173 | -0.919427493 | 0.659981637 | 315.1907849 | 30.24453177 | 1833.315466 |
9 | -1 | 0.65 | 0.714 | -0.803 | 79.5 | 7.35 | 448 | 9 | 0.571866178 | -0.945524396 | 0.689291949 | 273.9048972 | 22.6602808 | 1665.30474 |
9.5 | -1 | 0.633 | 0.716 | -0.84 | 69.2 | 5.47 | 406 | 9.5 | 0.573099177 | -0.977455448 | 0.712350288 | 238.7515604 | 17.41343565 | 1514.991934 |
10 | -1 | 0.625 | 0.727 | -0.867 | 60.5 | 4.25 | 369 | 10 | 0.578839688 | -1.000683008 | 0.734565322 | 208.6986492 | 13.25463367 | 1380.198191 |
10.5 | -1 | 0.626 | 0.742 | -0.893 | 53 | 3.29 | 336 | 10.5 | 0.588455603 | -1.026903911 | 0.755386914 | 182.9109323 | 10.10196054 | 1259.062284 |
11 | -1 | 0.643 | 0.769 | -0.905 | 46.5 | 2.61 | 306 | 11 | 0.597054452 | -1.052133963 | 0.775670911 | 160.707503 | 7.788443435 | 1149.985372 |
11.5 | -1 | 0.657 | 0.79 | -0.926 | 40.9 | 2.05 | 279 | 11.5 | 0.608963051 | -1.071230234 | 0.793960474 | 141.5296132 | 6.067481982 | 1051.587206 |
12 | -1 | 0.669 | 0.809 | -0.941 | 36.1 | 1.57 | 255 | 12 | 0.605496603 | -1.104019616 | 0.800156429 | 124.9160557 | 4.734398295 | 962.6709874 |
Modules
Unequal beta, module diff=14% | Identical beta, module diff=0.2% |
|---|---|
turquoise grey blue brown yellow green red pink magenta black purple | turquoise grey blue brown yellow green red black pink magenta purple |