Data is available on Synapse.

Summary

This includes code and plots for the final version of the paper. Exploratory analysis and intermediate processing steps are too extensive to be included here

## Warning: replacing previous import 'igraph::union' by 'GSEABase::union'
## when loading 'HTSanalyzeR'

WGCNA

##    Power SFT.R.sq  slope truncated.R.sq mean.k. median.k. max.k.
## 1      1   0.4680  2.380          0.871 4670.00  4780.000 6580.0
## 2      2   0.0044  0.118          0.700 1740.00  1770.000 3250.0
## 3      3   0.1660 -0.681          0.742  795.00   779.000 1870.0
## 4      4   0.3690 -1.090          0.808  411.00   382.000 1170.0
## 5      5   0.4980 -1.340          0.850  231.00   202.000  784.0
## 6      6   0.5850 -1.470          0.882  139.00   113.000  547.0
## 7      7   0.6460 -1.580          0.907   87.80    65.700  399.0
## 8      8   0.6630 -1.780          0.913   57.80    39.600  310.0
## 9      9   0.6920 -1.930          0.931   39.30    24.700  247.0
## 10    10   0.7120 -2.050          0.948   27.50    15.700  200.0
## 11    12   0.7770 -2.120          0.978   14.40     6.870  138.0
## 12    14   0.8220 -2.110          0.991    8.17     3.190   99.7
## 13    16   0.8590 -2.080          0.994    4.91     1.560   74.4
## 14    18   0.8860 -2.020          0.993    3.10     0.806   56.9
## 15    20   0.9030 -1.980          0.989    2.04     0.440   44.9
##    Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1      1   0.0710  1.02          0.894 4300.00  4340.000 6510.0
## 2      2   0.0808 -0.59          0.873 1490.00  1460.000 3100.0
## 3      3   0.3700 -1.08          0.900  639.00   593.000 1700.0
## 4      4   0.5650 -1.43          0.916  313.00   269.000 1060.0
## 5      5   0.6680 -1.62          0.929  169.00   132.000  709.0
## 6      6   0.7660 -1.69          0.968   97.70    68.700  505.0
## 7      7   0.8240 -1.81          0.985   60.00    37.400  390.0
## 8      8   0.8680 -1.86          0.995   38.60    21.200  311.0
## 9      9   0.9020 -1.87          0.998   25.90    12.500  254.0
## 10    10   0.9240 -1.86          0.996   17.90     7.560  213.0
## 11    12   0.9420 -1.85          0.988    9.35     2.950  159.0
## 12    14   0.9490 -1.79          0.979    5.35     1.260  124.0
## 13    16   0.9570 -1.71          0.976    3.30     0.580   99.6
## 14    18   0.9530 -1.66          0.966    2.16     0.286   81.5
## 15    20   0.9590 -1.59          0.969    1.49     0.146   67.7

Scale-free plot

## 6_wk_FB_neuron 
## TOM calculation: adjacency..
## adjacency: replaceMissing: 0
## ..will use 60 parallel threads.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication..
## ..normalization..
## ..done.
## NPC 
## TOM calculation: adjacency..
## adjacency: replaceMissing: 0
## ..will use 60 parallel threads.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication..
## ..normalization..
## ..done.
##           used  (Mb) gc trigger    (Mb)   max used    (Mb)
## Ncells 6603561 352.7    9968622   532.4    7998162   427.2
## Vcells 7421908  56.7 1494640669 11403.3 1705884830 13014.9

WGCNA.tree.plots

## 
 6_wk_FB_neuron                      
 NPC
## modulesInclude
## FALSE  TRUE 
##   952  5096
## setInclude
## TRUE 
## 6048
## 
## 0 - 1 1 - 2 2 - 3 3 - 4 4 - 5 5 - 6 6 - 7 
##  4043   289   121    86    62    52   443
## modulesInclude
## FALSE  TRUE 
##  3696  2352
## character(0)

color modules

Coexpression DE NPC

logFC AveExpr t P.Value adj.P.Val B
plum2 2.1705492 0 2.0834048 0.0440793 0.7539950 -4.576531
palevioletred3 -1.5744834 0 -1.9578668 0.0577116 0.7539950 -4.579167
lightpink4 -3.6318540 0 -1.8751967 0.0685628 0.7539950 -4.580846
brown4 -4.3894543 0 -1.7542441 0.0875520 0.7539950 -4.583216
darkgrey 2.3822910 0 1.7476297 0.0887069 0.7539950 -4.583343
firebrick4 4.6089558 0 1.7337877 0.0911652 0.7539950 -4.583606
salmon2 -1.0689715 0 -1.7123175 0.0950908 0.7539950 -4.584012
honeydew1 1.6311416 0 1.6988841 0.0976179 0.7539950 -4.584264
darkturquoise 5.1424736 0 1.6755085 0.1021483 0.7539950 -4.584699
cyan 4.0268696 0 1.6175620 0.1141328 0.7539950 -4.585759
brown -8.1230988 0 -1.5871205 0.1208763 0.7539950 -4.586305
mediumpurple3 -1.5580615 0 -1.5800384 0.1224908 0.7539950 -4.586431
tan -7.0254607 0 -1.5131427 0.1386202 0.7539950 -4.587599
plum 2.2587715 0 1.5016028 0.1415677 0.7539950 -4.587796
skyblue3 -3.2750342 0 -1.4580263 0.1531518 0.7539950 -4.588532
indianred4 2.7535250 0 1.4572086 0.1533761 0.7539950 -4.588545
plum3 1.0581336 0 1.4213573 0.1634700 0.7539950 -4.589137
skyblue1 0.8080262 0 1.4130403 0.1658845 0.7539950 -4.589273
brown2 -3.4221428 0 -1.3953123 0.1711243 0.7539950 -4.589560
darkolivegreen 1.7498363 0 1.3847454 0.1743083 0.7539950 -4.589729
mediumpurple4 -0.4728545 0 -1.3635939 0.1808196 0.7539950 -4.590066
thistle -0.6120084 0 -1.3392860 0.1885329 0.7539950 -4.590447
lightgreen -1.7148221 0 -1.3284778 0.1920425 0.7539950 -4.590615
magenta 9.4963195 0 1.2991241 0.2018264 0.7539950 -4.591065
violet 2.3697409 0 1.2862446 0.2062367 0.7539950 -4.591260
red 8.5412960 0 1.2520413 0.2183020 0.7539950 -4.591770
darkmagenta 8.5776073 0 1.2250513 0.2281895 0.7539950 -4.592164
yellow4 1.1182097 0 1.2135394 0.2325062 0.7539950 -4.592329
darkorange 2.3465659 0 1.2119454 0.2331087 0.7539950 -4.592352
black 4.6068302 0 1.2004646 0.2374819 0.7539950 -4.592516
darkgreen -2.3960168 0 -1.1900197 0.2415126 0.7539950 -4.592664
navajowhite2 2.2852294 0 1.1761588 0.2469386 0.7539950 -4.592859
honeydew 0.7545294 0 1.1493251 0.2576942 0.7539950 -4.593230
navajowhite1 0.7942679 0 1.1449620 0.2594746 0.7539950 -4.593290
orangered4 -0.9801040 0 -1.1373008 0.2626221 0.7539950 -4.593394
antiquewhite4 -1.0496474 0 -1.1188080 0.2703323 0.7539950 -4.593643
orange 3.5370460 0 1.1157007 0.2716436 0.7539950 -4.593685
paleturquoise -0.9391433 0 -1.0989813 0.2787767 0.7539950 -4.593906
maroon 0.7442825 0 1.0960165 0.2800553 0.7539950 -4.593945
pink4 0.4046986 0 1.0505403 0.3001879 0.7657926 -4.594532
blueviolet -0.6334805 0 -0.9780508 0.3343122 0.7657926 -4.595421
darkolivegreen2 -0.6666388 0 -0.9677789 0.3393506 0.7657926 -4.595542
darkseagreen4 0.6870247 0 0.9346146 0.3559620 0.7657926 -4.595926
saddlebrown 2.2372458 0 0.9280159 0.3593298 0.7657926 -4.596001
bisque4 -0.7497565 0 -0.9232670 0.3617664 0.7657926 -4.596055
blue2 -0.5932457 0 -0.9219864 0.3624253 0.7657926 -4.596069
royalblue 1.0609162 0 0.9125586 0.3673000 0.7657926 -4.596175
orangered3 0.9365543 0 0.8837751 0.3824445 0.7657926 -4.596491
lightcoral -0.5337747 0 -0.8780698 0.3854930 0.7657926 -4.596553
yellow3 0.3482152 0 0.8720311 0.3887364 0.7657926 -4.596618
lavenderblush3 0.7124621 0 0.8666759 0.3916272 0.7657926 -4.596675
sienna3 2.6207612 0 0.8409774 0.4056872 0.7657926 -4.596944
firebrick3 -0.6937629 0 -0.8286604 0.4125360 0.7657926 -4.597071
lightsteelblue1 0.6868805 0 0.8035190 0.4267351 0.7657926 -4.597324
salmon4 0.5645472 0 0.8025750 0.4272740 0.7657926 -4.597333
ivory 0.6966656 0 0.7772438 0.4418871 0.7657926 -4.597580
darkred 0.9067619 0 0.7765778 0.4422752 0.7657926 -4.597587
mediumorchid 0.6710831 0 0.7754606 0.4429268 0.7657926 -4.597597
blue -3.1195443 0 -0.7522735 0.4565793 0.7657926 -4.597817
floralwhite 0.6581960 0 0.7509486 0.4573667 0.7657926 -4.597829
grey60 -3.4419207 0 -0.7500484 0.4579022 0.7657926 -4.597837
lightyellow 1.7751060 0 0.7420318 0.4626871 0.7657926 -4.597911
coral 2.0127661 0 0.7342443 0.4673629 0.7657926 -4.597983
yellowgreen -0.9430046 0 -0.7280278 0.4711149 0.7657926 -4.598039
pink -1.7303582 0 -0.7231646 0.4740621 0.7657926 -4.598083
yellow 1.4208555 0 0.6953985 0.4910894 0.7812787 -4.598328
coral3 -0.5241966 0 -0.6513038 0.5188190 0.8064096 -4.598698
indianred3 0.2531523 0 0.6292378 0.5330053 0.8064096 -4.598874
steelblue 1.3975746 0 0.6238674 0.5364886 0.8064096 -4.598916
coral2 0.6931270 0 0.6221480 0.5376064 0.8064096 -4.598930
palevioletred2 0.5566436 0 0.5867169 0.5609069 0.8118529 -4.599198
skyblue4 -0.2382945 0 -0.5828181 0.5635016 0.8118529 -4.599226
white 0.5627355 0 0.5814238 0.5644310 0.8118529 -4.599236
green -0.9986547 0 -0.5413131 0.5914910 0.8392778 -4.599519
purple 1.3241429 0 0.5254976 0.6023287 0.8432602 -4.599625
darkslateblue -1.5410404 0 -0.5051148 0.6164318 0.8516492 -4.599757
darkseagreen3 -0.2308490 0 -0.4714462 0.6400515 0.8623555 -4.599965
salmon -1.3978017 0 -0.4691324 0.6416891 0.8623555 -4.599978
antiquewhite2 -0.2784340 0 -0.4590869 0.6488198 0.8623555 -4.600037
darkorange2 -1.5031840 0 -0.4197755 0.6770430 0.8758983 -4.600255
mediumpurple2 -0.2302104 0 -0.4191229 0.6775157 0.8758983 -4.600259
magenta4 0.2069893 0 0.4101406 0.6840348 0.8758983 -4.600306
mediumpurple1 -0.1418093 0 -0.3790922 0.7067559 0.8872082 -4.600461
thistle2 -0.4274062 0 -0.3744946 0.7101443 0.8872082 -4.600483
turquoise -1.2832287 0 -0.3634676 0.7182951 0.8872082 -4.600535
lightcyan 0.8514685 0 0.3521902 0.7266658 0.8872082 -4.600586
lightslateblue 0.4895761 0 0.3337402 0.7404333 0.8933958 -4.600666
skyblue2 -0.3670062 0 -0.3226504 0.7487508 0.8933958 -4.600712
thistle3 0.1255150 0 0.2705386 0.7882283 0.9275188 -4.600909
sienna4 0.7619266 0 0.2616577 0.7950161 0.9275188 -4.600939
greenyellow -0.4069919 0 -0.2372484 0.8137545 0.9389475 -4.601016
darkviolet 0.1258185 0 0.2222064 0.8253581 0.9419847 -4.601060
thistle1 -0.3981180 0 -0.1975816 0.8444388 0.9462225 -4.601126
lightsteelblue 0.1263598 0 0.1911300 0.8494540 0.9462225 -4.601142
coral1 -1.1348054 0 -0.1825855 0.8561060 0.9462225 -4.601162
plum1 -0.1842918 0 -0.1368728 0.8918630 0.9754751 -4.601255
grey -0.8411041 0 -0.1203059 0.9048826 0.9783833 -4.601282
lavenderblush2 0.1092837 0 0.1097940 0.9131577 0.9783833 -4.601298
lightblue4 0.0342797 0 0.0867172 0.9313573 0.9817407 -4.601327
orangered1 0.0265516 0 0.0613707 0.9513896 0.9817407 -4.601351
lightpink3 0.0421439 0 0.0540880 0.9571520 0.9817407 -4.601356
skyblue 0.0967230 0 0.0388689 0.9692010 0.9817407 -4.601365
darkolivegreen4 -0.0379890 0 -0.0328448 0.9739724 0.9817407 -4.601368
lightcyan1 -0.0254773 0 -0.0264437 0.9790436 0.9817407 -4.601370
midnightblue 0.0283294 0 0.0230396 0.9817407 0.9817407 -4.601371

Coexpression DE NPC

logFC AveExpr t P.Value adj.P.Val B
navajowhite1 4.8122794 0 2.0409968 0.0479893 0.9371373 -4.586815
saddlebrown -6.1762074 0 -2.0277737 0.0493833 0.9371373 -4.586946
violet -6.9688010 0 -1.9616493 0.0568954 0.9371373 -4.587594
orangered3 2.2004808 0 1.8189065 0.0765313 0.9371373 -4.588945
yellow3 3.9684493 0 1.7465508 0.0885072 0.9371373 -4.589603
magenta4 -7.5487178 0 -1.7136843 0.0944446 0.9371373 -4.589895
lavenderblush3 5.7526597 0 1.5908244 0.1196410 0.9371373 -4.590952
grey 8.7316614 0 1.5148921 0.1377809 0.9371373 -4.591576
mediumpurple3 -4.0522676 0 -1.4958639 0.1426560 0.9371373 -4.591728
skyblue4 1.7316975 0 1.4743397 0.1483353 0.9371373 -4.591899
blueviolet 1.7756474 0 1.4632927 0.1513191 0.9371373 -4.591986
bisque4 7.1191507 0 1.4573185 0.1529523 0.9371373 -4.592032
lightpink4 -2.0428168 0 -1.3678732 0.1791025 0.9371373 -4.592714
purple -3.5517984 0 -1.3242588 0.1930473 0.9371373 -4.593033
darkviolet -1.9551462 0 -1.2932144 0.2034674 0.9371373 -4.593255
indianred4 -1.3815277 0 -1.2065418 0.2348026 0.9371373 -4.593852
maroon -2.2728752 0 -1.1931572 0.2399425 0.9371373 -4.593941
brown2 1.1282429 0 1.1890744 0.2415267 0.9371373 -4.593968
sienna3 6.0620643 0 1.1715497 0.2484133 0.9371373 -4.594083
plum4 -0.9555364 0 -1.1345550 0.2634166 0.9371373 -4.594321
darkmagenta -1.6678715 0 -1.0809356 0.2862971 0.9371373 -4.594653
steelblue -1.4974662 0 -1.0482683 0.3009023 0.9371373 -4.594849
darkslateblue -2.2084275 0 -1.0223968 0.3128292 0.9371373 -4.595000
plum3 -1.3042397 0 -1.0216779 0.3131652 0.9371373 -4.595004
yellow4 -1.1534416 0 -1.0173604 0.3151881 0.9371373 -4.595029
darkturquoise -1.7156823 0 -1.0093899 0.3189460 0.9371373 -4.595075
lightgreen -1.9873219 0 -1.0001927 0.3233200 0.9371373 -4.595127
magenta -2.1835252 0 -0.9621029 0.3418651 0.9371373 -4.595339
yellowgreen -1.4593401 0 -0.9232311 0.3615058 0.9371373 -4.595548
firebrick4 0.9100228 0 0.9147529 0.3658853 0.9371373 -4.595592
skyblue -2.1649637 0 -0.8850512 0.3814980 0.9371373 -4.595745
palevioletred2 -0.7833286 0 -0.8836285 0.3822564 0.9371373 -4.595752
honeydew1 -0.8383654 0 -0.8390494 0.4065031 0.9371373 -4.595972
darkred -1.5565046 0 -0.8314668 0.4107203 0.9371373 -4.596009
orangered1 -0.5410850 0 -0.8264103 0.4135475 0.9371373 -4.596033
salmon1 1.0145211 0 0.8227751 0.4155874 0.9371373 -4.596050
plum2 -1.1859066 0 -0.8180152 0.4182677 0.9371373 -4.596073
red -2.1887415 0 -0.8019359 0.4274000 0.9371373 -4.596147
darkgrey -2.1809656 0 -0.7653092 0.4486472 0.9371373 -4.596313
lightpink3 0.8914472 0 0.7580297 0.4529431 0.9371373 -4.596345
coral -0.7514537 0 -0.7566477 0.4537614 0.9371373 -4.596351
deeppink 0.4403797 0 0.7543181 0.4551427 0.9371373 -4.596361
paleturquoise -1.0857683 0 -0.7452213 0.4605601 0.9371373 -4.596401
skyblue2 -0.8371630 0 -0.7436221 0.4615163 0.9371373 -4.596408
turquoise -3.5299241 0 -0.7385598 0.4645509 0.9371373 -4.596430
lightyellow -1.4899066 0 -0.7374757 0.4652022 0.9371373 -4.596434
lightsteelblue1 1.2231947 0 0.7360087 0.4660844 0.9371373 -4.596440
orange -1.2471930 0 -0.7256153 0.4723624 0.9371373 -4.596484
sienna4 -1.1775663 0 -0.7165214 0.4778949 0.9371373 -4.596522
darkolivegreen2 0.7027326 0 0.7128422 0.4801437 0.9371373 -4.596538
skyblue3 -1.4140012 0 -0.7024506 0.4865274 0.9371373 -4.596580
darkseagreen4 -0.8903241 0 -0.6642078 0.5104255 0.9371373 -4.596732
darkorange -1.2718729 0 -0.6472471 0.5212251 0.9371373 -4.596797
mediumpurple2 -1.3319793 0 -0.6451764 0.5225519 0.9371373 -4.596805
darkgreen -0.9906970 0 -0.6399076 0.5259361 0.9371373 -4.596825
darkolivegreen -0.9911397 0 -0.6291378 0.5328895 0.9371373 -4.596864
ivory -0.7768885 0 -0.6182480 0.5399692 0.9371373 -4.596904
brown -4.1788250 0 -0.6074546 0.5470342 0.9371373 -4.596943
darkorange2 -0.8677346 0 -0.6017069 0.5508157 0.9371373 -4.596963
thistle 0.7368926 0 0.5934359 0.5562807 0.9371373 -4.596992
cyan -1.3783022 0 -0.5827025 0.5634135 0.9371373 -4.597029
thistle4 -0.4926345 0 -0.5309679 0.5984213 0.9371373 -4.597198
pink4 -0.4244169 0 -0.5117732 0.6116660 0.9371373 -4.597257
darkolivegreen4 -0.5077839 0 -0.4797506 0.6340570 0.9371373 -4.597350
coral1 -0.6225239 0 -0.4766954 0.6362120 0.9371373 -4.597358
floralwhite -0.7379744 0 -0.4750672 0.6373618 0.9371373 -4.597363
plum1 -0.7119598 0 -0.4615426 0.6469472 0.9371373 -4.597400
salmon4 -0.6615917 0 -0.4512737 0.6542662 0.9371373 -4.597428
antiquewhite4 -0.5705543 0 -0.4506312 0.6547253 0.9371373 -4.597430
greenyellow -2.3025906 0 -0.4455723 0.6583447 0.9371373 -4.597443
lightslateblue 0.7019880 0 0.4403951 0.6620575 0.9371373 -4.597456
plum -0.5499933 0 -0.4394467 0.6627385 0.9371373 -4.597459
thistle3 -0.4877405 0 -0.4203376 0.6765223 0.9371373 -4.597507
midnightblue -1.0225278 0 -0.4174980 0.6785803 0.9371373 -4.597514
honeydew 2.3299323 0 0.3971516 0.6933988 0.9371373 -4.597563
navajowhite2 -0.5285588 0 -0.3944744 0.6953579 0.9371373 -4.597570
blue4 -0.9766020 0 -0.3915395 0.6975079 0.9371373 -4.597576
mediumpurple4 -0.3379498 0 -0.3825527 0.7041072 0.9371373 -4.597597
thistle2 0.5104200 0 0.3611922 0.7198852 0.9371373 -4.597644
indianred3 -0.2228144 0 -0.3576398 0.7225215 0.9371373 -4.597651
royalblue -0.6602178 0 -0.3571204 0.7229072 0.9371373 -4.597652
grey60 -0.6814537 0 -0.3527224 0.7261764 0.9371373 -4.597662
lightcyan -0.5914186 0 -0.3414321 0.7345924 0.9371373 -4.597685
lightsteelblue -0.3734136 0 -0.3389409 0.7364539 0.9371373 -4.597690
mediumpurple1 0.2675987 0 0.3261862 0.7460096 0.9371373 -4.597715
antiquewhite2 -0.2303870 0 -0.3226407 0.7486732 0.9371373 -4.597722
tan4 0.2005924 0 0.3192949 0.7511895 0.9371373 -4.597728
darkseagreen3 0.2753627 0 0.3154697 0.7540698 0.9371373 -4.597735
tan -0.7481624 0 -0.3115783 0.7570037 0.9371373 -4.597743
brown4 -0.5304712 0 -0.3078193 0.7598411 0.9371373 -4.597749
orangered4 -0.5008488 0 -0.2953093 0.7693081 0.9383868 -4.597772
white -0.4622723 0 -0.2752247 0.7845817 0.9396957 -4.597806
blue 0.9220952 0 0.2444494 0.8081512 0.9396957 -4.597853
mediumorchid -0.3224365 0 -0.2347236 0.8156387 0.9396957 -4.597867
lightcyan1 0.5297392 0 0.2340580 0.8161518 0.9396957 -4.597868
salmon2 -0.2268325 0 -0.2185547 0.8281249 0.9396957 -4.597889
coral2 0.2469113 0 0.2039253 0.8394615 0.9396957 -4.597907
firebrick3 -0.1458260 0 -0.2023888 0.8406542 0.9396957 -4.597909
blue2 0.2053367 0 0.2019042 0.8410304 0.9396957 -4.597910
palevioletred3 0.2192199 0 0.1884715 0.8514744 0.9396957 -4.597925
lightcoral 0.3584519 0 0.1838956 0.8550384 0.9396957 -4.597930
salmon 0.4055484 0 0.1651725 0.8696527 0.9463868 -4.597950
coral3 0.1649238 0 0.1222644 0.9033111 0.9652057 -4.597986
pink -0.2895193 0 -0.1209607 0.9043368 0.9652057 -4.597987
yellow 0.4549620 0 0.1031343 0.9183795 0.9689569 -4.597999
lightblue4 -0.0452934 0 -0.0943489 0.9253101 0.9689569 -4.598004
skyblue1 -0.1043484 0 -0.0664073 0.9473893 0.9828057 -4.598018
black -0.1781231 0 -0.0511964 0.9594277 0.9860784 -4.598023
green 0.1175582 0 0.0358459 0.9715862 0.9867908 -4.598027
thistle1 0.0443091 0 0.0278773 0.9779008 0.9867908 -4.598029
lavenderblush2 0.0029209 0 0.0029049 0.9976969 0.9976969 -4.598031