Mouse cell gene expression
Thomas Källman
23 Apr 2015
A brief summary of the gene expression analysis done for the mouse data. Mostly to try out the share function on rpub.
library(limma)
library(edgeR)
library(biomaRt)## Warning: package 'biomaRt' was built under R version 3.2.2## Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'rm(list = ls())
# make Mouse genome info from ensembl avaialbe via biomart
mart <- useMart("ensembl", dataset="mmusculus_gene_ensembl")
# Read data on counts into R and convert to suitable format
counts<-read.table("../counts/count_table.txt")
y <- DGEList(counts=counts)
# Extract external gene names for all ensembl gene ids in y
gene.list <- getBM(attributes = c("ensembl_gene_id", "external_gene_name"), filters = "ensembl_gene_id", values = row.names(y$counts), uniqueRows=FALSE, mart=mart)
# Filter away gene models that is no longer supported in ensembl from y
index <- row.names(y$counts) %in% gene.list$ensembl_gene_id
y$counts <- y$counts[index,]
# Filter away genes that have an average expression lower than 39 reads over all samples and re-estimate norm factors eg. depth of sequencing
A <- rowSums(y$counts)
isexpr <- A > 39
y<-y[isexpr,,keep.lib.size = FALSE]
y<-(calcNormFactors(y))
# Make sure that that the gene.list is identical to y
gene.list.retained <- gene.list[gene.list[,1] %in% row.names(y),]
gene.list.retained <- gene.list.retained[order(gene.list.retained$ensembl_gene_id),]
# Create model matrix for Limma analysis
design<-read.table("../designMatrix.txt", header=T)
lev <- c("con.0d","con.1d","CeO2.1d","SDC.1d","NAC.1d","con.4d","CeO2.4d","SDC.4d","NAC.4d", "con.7d","CeO2.7d","SDC.7d","NAC.7d")
f<- factor(design$Name, levels=lev)
des <- model.matrix(~0+f)
colnames(des) <- lev
# Transform count data for Linear modelling using Limma
v<-voom(y, des, plot = TRUE)
# Do the actual linear modelling and calc. associated stats
fit <- lmFit(v, des)
# save(list = c('fit', 'gene.list.retained'), file = "Fit.rdata")
load('Fit.rdata')
# Extract contrasts of interest and detect DE genes within these. Extracted contrasts are all 4 over time, indivdual treatments for all time points eg. CeO2day1-controlday1 etc
control.time <- makeContrasts("con.7d-con.4d", "con.4d-con.1d", "con.1d-con.0d", levels=lev)
fit.control.time <- contrasts.fit(fit, control.time)
fit.control.time <- eBayes(fit.control.time)
fit.control.time$genes <- gene.list.retained
topTableF(fit.control.time, adjust="BH")## ensembl_gene_id external_gene_name con.7d.con.4d
## ENSMUSG00000026185 ENSMUSG00000026185 Igfbp5 -0.04205797
## ENSMUSG00000022324 ENSMUSG00000022324 Matn2 1.40439503
## ENSMUSG00000018411 ENSMUSG00000018411 Mapt 0.43925052
## ENSMUSG00000024063 ENSMUSG00000024063 Lbh 0.60381883
## ENSMUSG00000052229 ENSMUSG00000052229 Gpr17 0.34745599
## ENSMUSG00000022325 ENSMUSG00000022325 Pop1 -1.56908119
## ENSMUSG00000033208 ENSMUSG00000033208 S100b 1.05044113
## ENSMUSG00000030257 ENSMUSG00000030257 Srgap3 0.88007872
## ENSMUSG00000039883 ENSMUSG00000039883 Lrrc17 0.84198965
## ENSMUSG00000031375 ENSMUSG00000031375 Bgn 3.13683269
## con.4d.con.1d con.1d.con.0d AveExpr F
## ENSMUSG00000026185 3.3435759 1.9348107 6.848453 1035.3012
## ENSMUSG00000022324 0.9556118 2.0653962 8.564492 824.7143
## ENSMUSG00000018411 2.2370467 2.4951980 5.959252 729.3101
## ENSMUSG00000024063 0.8014140 1.5521724 8.965534 666.5388
## ENSMUSG00000052229 2.5955381 3.3561549 6.365094 630.1308
## ENSMUSG00000022325 -0.1412018 -1.1207095 5.644061 598.1221
## ENSMUSG00000033208 1.0198146 2.5754579 6.865381 579.8498
## ENSMUSG00000030257 1.4916182 0.3321781 5.387324 573.2043
## ENSMUSG00000039883 1.2124879 3.9386574 5.183537 557.9930
## ENSMUSG00000031375 0.5325526 0.2725181 5.332354 520.9933
## P.Value adj.P.Val
## ENSMUSG00000026185 6.991980e-31 1.233106e-26
## ENSMUSG00000022324 2.194739e-29 1.935321e-25
## ENSMUSG00000018411 1.408679e-28 8.281152e-25
## ENSMUSG00000024063 5.483129e-28 2.417512e-24
## ENSMUSG00000052229 1.279318e-27 4.512410e-24
## ENSMUSG00000022325 2.806530e-27 8.249328e-24
## ENSMUSG00000033208 4.477951e-27 1.128188e-23
## ENSMUSG00000030257 5.326446e-27 1.174215e-23
## ENSMUSG00000039883 7.983779e-27 1.564466e-23
## ENSMUSG00000031375 2.239688e-26 3.800628e-23results.control.time <- decideTests(fit.control.time, adjust.method="BH")
write.fit(fit.control.time, results=results.control.time, file="Control_overtime.txt", digits=30, dec=",", adjust = "BH")
control.time70 <- makeContrasts("con.7d-con.0d", levels=lev)
fit.control.time70 <- contrasts.fit(fit, control.time70)
fit.control.time70 <- eBayes(fit.control.time70)
fit.control.time70$genes <- gene.list.retained
topTableF(fit.control.time70, adjust="BH")## ensembl_gene_id external_gene_name con.7d.con.0d
## ENSMUSG00000022324 ENSMUSG00000022324 Matn2 4.425403
## ENSMUSG00000024063 ENSMUSG00000024063 Lbh 2.957405
## ENSMUSG00000022325 ENSMUSG00000022325 Pop1 -2.830992
## ENSMUSG00000026185 ENSMUSG00000026185 Igfbp5 5.236329
## ENSMUSG00000022548 ENSMUSG00000022548 Apod 3.231400
## ENSMUSG00000033208 ENSMUSG00000033208 S100b 4.645714
## ENSMUSG00000027800 ENSMUSG00000027800 Tm4sf1 -3.307508
## ENSMUSG00000011179 ENSMUSG00000011179 Odc1 -3.503290
## ENSMUSG00000017466 ENSMUSG00000017466 Timp2 2.423630
## ENSMUSG00000030257 ENSMUSG00000030257 Srgap3 2.703875
## AveExpr F P.Value adj.P.Val
## ENSMUSG00000022324 8.564492 2249.275 2.967333e-30 5.233189e-26
## ENSMUSG00000024063 8.965534 1764.924 1.155931e-28 1.019300e-24
## ENSMUSG00000022325 5.644061 1713.152 1.810519e-28 1.064344e-24
## ENSMUSG00000026185 6.848453 1589.645 5.586034e-28 2.462882e-24
## ENSMUSG00000022548 6.465864 1340.281 7.249830e-27 2.070700e-23
## ENSMUSG00000033208 6.865381 1320.665 9.043446e-27 2.070700e-23
## ENSMUSG00000027800 7.725035 1318.275 9.292431e-27 2.070700e-23
## ENSMUSG00000011179 6.361412 1317.328 9.393062e-27 2.070700e-23
## ENSMUSG00000017466 9.510331 1229.194 2.650151e-26 5.193117e-23
## ENSMUSG00000030257 5.387324 1159.370 6.355296e-26 1.120820e-22results.control.time70 <- decideTests(fit.control.time70, adjust.method="BH")
write.fit(fit.control.time70, results=results.control.time70, file="Control.time70.txt", digits=30, dec=",", adjust = "BH")
control.time71 <- makeContrasts("con.7d-con.1d", levels=lev)
fit.control.time71 <- contrasts.fit(fit, control.time71)
fit.control.time71 <- eBayes(fit.control.time71)
fit.control.time71$genes <- gene.list.retained
topTableF(fit.control.time71, adjust="BH")## ensembl_gene_id external_gene_name con.7d.con.1d
## ENSMUSG00000001864 ENSMUSG00000001864 Aif1l -2.643746
## ENSMUSG00000028364 ENSMUSG00000028364 Tnc 4.660867
## ENSMUSG00000030257 ENSMUSG00000030257 Srgap3 2.371697
## ENSMUSG00000031375 ENSMUSG00000031375 Bgn 3.669385
## ENSMUSG00000026185 ENSMUSG00000026185 Igfbp5 3.301518
## ENSMUSG00000025978 ENSMUSG00000025978 Rftn2 1.815992
## ENSMUSG00000035493 ENSMUSG00000035493 Tgfbi 2.737090
## ENSMUSG00000069910 ENSMUSG00000069910 Spdl1 -2.273209
## ENSMUSG00000017716 ENSMUSG00000017716 Birc5 -2.535744
## ENSMUSG00000039748 ENSMUSG00000039748 Exo1 -2.616656
## AveExpr F P.Value adj.P.Val
## ENSMUSG00000001864 5.574066 1118.9150 1.080361e-25 1.401037e-21
## ENSMUSG00000028364 8.470727 1090.3733 1.588838e-25 1.401037e-21
## ENSMUSG00000030257 5.387324 985.1254 7.210836e-25 3.849663e-21
## ENSMUSG00000031375 5.332354 972.5366 8.731375e-25 3.849663e-21
## ENSMUSG00000026185 6.848453 957.8022 1.095667e-24 3.864638e-21
## ENSMUSG00000025978 6.295899 934.4058 1.582344e-24 4.651037e-21
## ENSMUSG00000035493 7.955551 818.4572 1.128012e-23 2.689136e-20
## ENSMUSG00000069910 4.788107 814.1379 1.219839e-23 2.689136e-20
## ENSMUSG00000017716 6.039535 797.0584 1.668890e-23 3.215431e-20
## ENSMUSG00000039748 5.043317 792.3018 1.823220e-23 3.215431e-20results.control.time71 <- decideTests(fit.control.time71, adjust.method="BH")
write.fit(fit.control.time71, results=results.control.time71, file="Control.time71.txt", digits=30, dec=",", adjust = "BH")
control.time40 <- makeContrasts("con.4d-con.0d", levels=lev)
fit.control.time40 <- contrasts.fit(fit, control.time40)
fit.control.time40 <- eBayes(fit.control.time40)
fit.control.time40$genes <- gene.list.retained
topTableF(fit.control.time40, adjust="BH")## ensembl_gene_id external_gene_name con.4d.con.0d
## ENSMUSG00000026185 ENSMUSG00000026185 Igfbp5 5.278387
## ENSMUSG00000024063 ENSMUSG00000024063 Lbh 2.353586
## ENSMUSG00000022324 ENSMUSG00000022324 Matn2 3.021008
## ENSMUSG00000018166 ENSMUSG00000018166 Erbb3 2.255190
## ENSMUSG00000018411 ENSMUSG00000018411 Mapt 4.732245
## ENSMUSG00000025880 ENSMUSG00000025880 Smad7 -3.369375
## ENSMUSG00000042961 ENSMUSG00000042961 Egflam 3.665236
## ENSMUSG00000033066 ENSMUSG00000033066 Gas7 2.856067
## ENSMUSG00000018217 ENSMUSG00000018217 Pmp22 2.167775
## ENSMUSG00000033208 ENSMUSG00000033208 S100b 3.595272
## AveExpr F P.Value adj.P.Val
## ENSMUSG00000026185 6.848453 1612.1910 4.519152e-28 7.969977e-24
## ENSMUSG00000024063 8.965534 1110.6406 1.206976e-25 1.064312e-21
## ENSMUSG00000022324 8.564492 1036.5815 3.378470e-25 1.986090e-21
## ENSMUSG00000018166 8.995420 975.7195 8.317153e-25 3.667033e-21
## ENSMUSG00000018411 5.959252 936.2193 1.537413e-24 5.422762e-21
## ENSMUSG00000025880 3.092117 900.4757 2.740373e-24 7.337873e-21
## ENSMUSG00000042961 5.772126 896.7861 2.912515e-24 7.337873e-21
## ENSMUSG00000033066 9.678186 865.9955 4.889556e-24 1.077903e-20
## ENSMUSG00000018217 6.658928 809.0147 1.339194e-23 2.624226e-20
## ENSMUSG00000033208 6.865381 779.8545 2.303654e-23 3.773546e-20results.control.time40 <- decideTests(fit.control.time40, adjust.method="BH")
write.fit(fit.control.time40, results=results.control.time40, file="control.time40.txt", digits=30, dec=",", adjust = "BH")
CeO2.time <- makeContrasts("CeO2.7d-CeO2.4d", "CeO2.4d-CeO2.1d", "CeO2.1d-con.0d", levels=lev)
fit.CeO2.time <- contrasts.fit(fit, CeO2.time)
fit.CeO2.time <- eBayes(fit.CeO2.time)
fit.CeO2.time$genes <- gene.list.retained
topTableF(fit.CeO2.time, adjust="BH")## ensembl_gene_id external_gene_name CeO2.7d.CeO2.4d
## ENSMUSG00000026185 ENSMUSG00000026185 Igfbp5 1.1508755
## ENSMUSG00000018411 ENSMUSG00000018411 Mapt 0.4084504
## ENSMUSG00000022324 ENSMUSG00000022324 Matn2 1.5986749
## ENSMUSG00000030257 ENSMUSG00000030257 Srgap3 1.2827304
## ENSMUSG00000064373 ENSMUSG00000064373 Sepp1 1.4726946
## ENSMUSG00000019929 ENSMUSG00000019929 Dcn 2.3520543
## ENSMUSG00000031375 ENSMUSG00000031375 Bgn 3.2014257
## ENSMUSG00000052229 ENSMUSG00000052229 Gpr17 0.2916283
## ENSMUSG00000039883 ENSMUSG00000039883 Lrrc17 0.6454931
## ENSMUSG00000041577 ENSMUSG00000041577 Prelp 1.2301313
## CeO2.4d.CeO2.1d CeO2.1d.con.0d AveExpr F
## ENSMUSG00000026185 2.3009257 1.73992801 6.848453 823.9185
## ENSMUSG00000018411 1.8622713 2.96394913 5.959252 703.3708
## ENSMUSG00000022324 0.5777037 1.83082116 8.564492 651.2860
## ENSMUSG00000030257 1.5043358 0.04310710 5.387324 650.4176
## ENSMUSG00000064373 2.2044718 3.01982128 5.748744 638.2261
## ENSMUSG00000019929 2.7729172 2.83945063 4.126106 614.9391
## ENSMUSG00000031375 0.9506854 -0.03720565 5.332354 602.8588
## ENSMUSG00000052229 3.0020417 2.61408547 6.365094 575.2719
## ENSMUSG00000039883 1.3466657 4.02772333 5.183537 572.8416
## ENSMUSG00000041577 2.1889261 0.25195870 5.943840 553.4755
## P.Value adj.P.Val
## ENSMUSG00000026185 2.227041e-29 3.927610e-25
## ENSMUSG00000018411 2.434443e-28 2.146692e-24
## ENSMUSG00000022324 7.775169e-28 3.497762e-24
## ENSMUSG00000030257 7.933232e-28 3.497762e-24
## ENSMUSG00000064373 1.055329e-27 3.722356e-24
## ENSMUSG00000019929 1.848137e-27 5.432289e-24
## ENSMUSG00000031375 2.492090e-27 6.278642e-24
## ENSMUSG00000052229 5.045454e-27 1.053738e-23
## ENSMUSG00000039883 5.377435e-27 1.053738e-23
## ENSMUSG00000041577 9.022291e-27 1.591171e-23results.CeO2.time <- decideTests(fit.CeO2.time, adjust.method="BH")
summary(results.CeO2.time)## CeO2.7d-CeO2.4d CeO2.4d-CeO2.1d CeO2.1d-con.0d
## -1 4298 4367 2793
## 0 9621 8443 11350
## 1 3717 4826 3493write.fit(fit.CeO2.time, results=results.CeO2.time, file="CeO2_overtime.txt", digits=30, dec=",", adjust = "BH")
NAC.time <- makeContrasts("NAC.7d-NAC.4d", "NAC.4d-NAC.1d", "NAC.1d-con.0d", levels=lev)
fit.NAC.time <- contrasts.fit(fit, NAC.time)
fit.NAC.time <- eBayes(fit.NAC.time)
fit.NAC.time$genes <- gene.list.retained
topTableF(fit.NAC.time, adjust="BH")## ensembl_gene_id external_gene_name NAC.7d.NAC.4d
## ENSMUSG00000018411 ENSMUSG00000018411 Mapt 0.83261518
## ENSMUSG00000022324 ENSMUSG00000022324 Matn2 0.87713221
## ENSMUSG00000026185 ENSMUSG00000026185 Igfbp5 0.45783616
## ENSMUSG00000052229 ENSMUSG00000052229 Gpr17 0.57393674
## ENSMUSG00000024063 ENSMUSG00000024063 Lbh 0.09732397
## ENSMUSG00000041577 ENSMUSG00000041577 Prelp 1.53787331
## ENSMUSG00000033208 ENSMUSG00000033208 S100b 0.90161227
## ENSMUSG00000022325 ENSMUSG00000022325 Pop1 -1.21119698
## ENSMUSG00000017466 ENSMUSG00000017466 Timp2 0.93638317
## ENSMUSG00000042961 ENSMUSG00000042961 Egflam 0.13856860
## NAC.4d.NAC.1d NAC.1d.con.0d AveExpr F
## ENSMUSG00000018411 1.523903782 3.098878 5.959252 735.1090
## ENSMUSG00000022324 0.768273260 2.086107 8.564492 599.1931
## ENSMUSG00000026185 1.690595445 2.258173 6.848453 579.1697
## ENSMUSG00000052229 1.923190127 3.772413 6.365094 564.8518
## ENSMUSG00000024063 0.357658411 1.980076 8.965534 525.5223
## ENSMUSG00000041577 0.892998189 1.525438 5.943840 525.4411
## ENSMUSG00000033208 0.947557978 2.466259 6.865381 501.8273
## ENSMUSG00000022325 -0.001025374 -1.308635 5.644061 488.0648
## ENSMUSG00000017466 0.035047667 1.566587 9.510331 464.7834
## ENSMUSG00000042961 1.025843637 2.535757 5.772126 463.3672
## P.Value adj.P.Val
## ENSMUSG00000018411 1.249790e-28 2.204130e-24
## ENSMUSG00000022324 2.731913e-27 2.409001e-23
## ENSMUSG00000026185 4.557771e-27 2.679362e-23
## ENSMUSG00000052229 6.643211e-27 2.928992e-23
## ENSMUSG00000024063 1.966553e-26 5.793791e-23
## ENSMUSG00000041577 1.971124e-26 5.793791e-23
## ENSMUSG00000033208 3.932441e-26 9.907504e-23
## ENSMUSG00000022325 5.969259e-26 1.315923e-22
## ENSMUSG00000017466 1.242373e-25 2.171840e-22
## ENSMUSG00000042961 1.300516e-25 2.171840e-22results.NAC.time <- decideTests(fit.NAC.time, adjust.method="BH")
write.fit(fit.NAC.time, results = results.NAC.time, file="NAC_overtime.txt", digits=30, dec=",", adjust = "BH")
SDC.time <- makeContrasts("SDC.7d-SDC.4d", "SDC.4d-SDC.1d", "SDC.1d-con.0d", levels=lev)
fit.SDC.time <- contrasts.fit(fit, SDC.time)
fit.SDC.time <- eBayes(fit.SDC.time)
fit.SDC.time$genes <- gene.list.retained
topTableF(fit.SDC.time, adjust="BH")## ensembl_gene_id external_gene_name SDC.7d.SDC.4d
## ENSMUSG00000026185 ENSMUSG00000026185 Igfbp5 1.1416102
## ENSMUSG00000031375 ENSMUSG00000031375 Bgn 3.1872134
## ENSMUSG00000018411 ENSMUSG00000018411 Mapt 0.4131721
## ENSMUSG00000064373 ENSMUSG00000064373 Sepp1 0.9544170
## ENSMUSG00000052229 ENSMUSG00000052229 Gpr17 0.9049000
## ENSMUSG00000041577 ENSMUSG00000041577 Prelp 1.3640240
## ENSMUSG00000022324 ENSMUSG00000022324 Matn2 1.4997120
## ENSMUSG00000039883 ENSMUSG00000039883 Lrrc17 0.4329990
## ENSMUSG00000022325 ENSMUSG00000022325 Pop1 -1.2007873
## ENSMUSG00000019929 ENSMUSG00000019929 Dcn 1.7383878
## SDC.4d.SDC.1d SDC.1d.con.0d AveExpr F
## ENSMUSG00000026185 2.7354232 1.3417178 6.848453 895.1869
## ENSMUSG00000031375 1.3382123 -0.1072322 5.332354 729.0245
## ENSMUSG00000018411 1.9676238 2.8403802 5.959252 725.4111
## ENSMUSG00000064373 2.7380236 2.7045786 5.748744 626.7169
## ENSMUSG00000052229 2.5080690 2.8606063 6.365094 615.3814
## ENSMUSG00000041577 1.9696730 0.5543722 5.943840 607.9050
## ENSMUSG00000022324 0.6430222 1.7020453 8.564492 604.9159
## ENSMUSG00000039883 1.6602202 3.8042914 5.183537 597.9337
## ENSMUSG00000022325 -0.3457078 -1.2287068 5.644061 585.1358
## ENSMUSG00000019929 3.7742801 2.0252635 4.126106 546.9591
## P.Value adj.P.Val
## ENSMUSG00000026185 6.340862e-30 1.118274e-25
## ENSMUSG00000031375 1.417039e-28 8.979789e-25
## ENSMUSG00000018411 1.527521e-28 8.979789e-25
## ENSMUSG00000064373 1.388499e-27 5.964559e-24
## ENSMUSG00000052229 1.828219e-27 5.964559e-24
## ENSMUSG00000041577 2.197974e-27 5.964559e-24
## ENSMUSG00000022324 2.367425e-27 5.964559e-24
## ENSMUSG00000039883 2.819879e-27 6.216424e-24
## ENSMUSG00000022325 3.906080e-27 7.654180e-24
## ENSMUSG00000019929 1.078146e-26 1.901418e-23results.SDC.time <- decideTests(fit.SDC.time, adjust.method="BH")
write.fit(fit.SDC.time, results = results.SDC.time, file="SDC_overtime.txt", digits=30, dec=",", adjust = "BH")
CeO2.time1 <- makeContrasts(CeO2.1d-con.1d, levels=lev)
fit.CeO2.time1 <- contrasts.fit(fit, CeO2.time1)
fit.CeO2.time1 <- eBayes(fit.CeO2.time1)
fit.CeO2.time1$genes <- gene.list.retained
topTableF(fit.CeO2.time1, adjust="BH")## ensembl_gene_id external_gene_name CeO2.1d...con.1d
## ENSMUSG00000090290 ENSMUSG00000090290 Gm17296 -0.9147794
## ENSMUSG00000060429 ENSMUSG00000060429 Sntb1 -1.0867815
## ENSMUSG00000021273 ENSMUSG00000021273 Fdft1 0.8550144
## ENSMUSG00000023832 ENSMUSG00000023832 Acat2 1.0614358
## ENSMUSG00000060012 ENSMUSG00000060012 Kif13b -1.2904199
## ENSMUSG00000001962 ENSMUSG00000001962 Fam50a 0.8205950
## ENSMUSG00000026131 ENSMUSG00000026131 Dst -0.8104481
## ENSMUSG00000021114 ENSMUSG00000021114 Atp6v1d 0.8996911
## ENSMUSG00000038914 ENSMUSG00000038914 Dido1 -0.6636388
## ENSMUSG00000031458 ENSMUSG00000031458 Coprs 1.1890885
## AveExpr F P.Value adj.P.Val
## ENSMUSG00000090290 5.134911 144.1298 4.038592e-13 4.492169e-09
## ENSMUSG00000060429 7.109735 141.5186 5.094317e-13 4.492169e-09
## ENSMUSG00000021273 7.032517 132.6478 1.152400e-12 6.774576e-09
## ENSMUSG00000023832 7.684751 128.2707 1.752882e-12 7.728456e-09
## ENSMUSG00000060012 4.303778 115.8338 6.170764e-12 1.845864e-08
## ENSMUSG00000001962 5.610451 115.2647 6.553268e-12 1.845864e-08
## ENSMUSG00000026131 9.339188 114.2152 7.326518e-12 1.845864e-08
## ENSMUSG00000021114 5.848424 111.9203 9.376991e-12 2.007463e-08
## ENSMUSG00000038914 6.437620 111.1064 1.024448e-11 2.007463e-08
## ENSMUSG00000031458 3.974451 104.5139 2.139033e-11 3.772399e-08results.CeO2.time1 <- decideTests(fit.CeO2.time1, adjust.method="BH")
summary(results.CeO2.time1)## CeO2.1d - con.1d
## -1 1585
## 0 13686
## 1 2365write.fit(fit.CeO2.time1, results=results.CeO2.time1, file="CeO2_time1.txt", digits=30, dec=",", adjust="BH")
NAC.time1 <- makeContrasts(NAC.1d-con.1d, levels=lev)
fit.NAC.time1 <- contrasts.fit(fit, NAC.time1)
fit.NAC.time1 <- eBayes(fit.NAC.time1)
fit.NAC.time1$genes <- gene.list.retained
topTableF(fit.NAC.time1, adjust="BH")## ensembl_gene_id external_gene_name NAC.1d...con.1d
## ENSMUSG00000024190 ENSMUSG00000024190 Dusp1 2.0923603
## ENSMUSG00000019970 ENSMUSG00000019970 Sgk1 1.3886134
## ENSMUSG00000028124 ENSMUSG00000028124 Gclm -1.1812731
## ENSMUSG00000019997 ENSMUSG00000019997 Ctgf 2.0787289
## ENSMUSG00000024803 ENSMUSG00000024803 Ankrd1 1.3053537
## ENSMUSG00000031400 ENSMUSG00000031400 G6pdx -0.9532982
## ENSMUSG00000021367 ENSMUSG00000021367 Edn1 1.8603920
## ENSMUSG00000032802 ENSMUSG00000032802 Srxn1 -0.9492355
## ENSMUSG00000043079 ENSMUSG00000043079 Synpo 1.1412116
## ENSMUSG00000021250 ENSMUSG00000021250 Fos 3.2151637
## AveExpr F P.Value adj.P.Val
## ENSMUSG00000024190 5.248028 161.26309 9.548250e-14 1.104379e-09
## ENSMUSG00000019970 6.431186 154.75769 1.624938e-13 1.104379e-09
## ENSMUSG00000028124 6.175399 150.06583 2.412678e-13 1.104379e-09
## ENSMUSG00000019997 5.398320 149.62715 2.504829e-13 1.104379e-09
## ENSMUSG00000024803 4.747288 133.87081 1.027042e-12 3.508576e-09
## ENSMUSG00000031400 7.157140 132.27603 1.193664e-12 3.508576e-09
## ENSMUSG00000021367 1.941905 117.59844 5.128541e-12 1.267397e-08
## ENSMUSG00000032802 5.195534 116.50634 5.749137e-12 1.267397e-08
## ENSMUSG00000043079 5.092500 106.35081 1.736091e-11 3.401967e-08
## ENSMUSG00000021250 4.182350 99.15192 4.000511e-11 7.055301e-08results.NAC.time1 <- decideTests(fit.NAC.time1, adjust.method="BH")
summary(results.NAC.time1)## NAC.1d - con.1d
## -1 843
## 0 15772
## 1 1021write.fit(fit.NAC.time1, results=results.NAC.time1, file="NAC_time1.txt", digits=30, dec=",", adjust="BH")
SDC.time1 <- makeContrasts(SDC.1d-con.1d, levels=lev)
fit.SDC.time1 <- contrasts.fit(fit, SDC.time1)
fit.SDC.time1 <- eBayes(fit.SDC.time1)
fit.SDC.time1$genes <- gene.list.retained
topTableF(fit.SDC.time1, adjust="BH")## ensembl_gene_id external_gene_name SDC.1d...con.1d
## ENSMUSG00000029816 ENSMUSG00000029816 Gpnmb 1.9164095
## ENSMUSG00000024066 ENSMUSG00000024066 Xdh 1.1769875
## ENSMUSG00000060429 ENSMUSG00000060429 Sntb1 -0.7831405
## ENSMUSG00000028364 ENSMUSG00000028364 Tnc -1.2238416
## ENSMUSG00000038244 ENSMUSG00000038244 Mical2 -0.6558224
## ENSMUSG00000041779 ENSMUSG00000041779 Tram2 -0.6081935
## ENSMUSG00000000171 ENSMUSG00000000171 Sdhd 0.4891848
## ENSMUSG00000022816 ENSMUSG00000022816 Fstl1 -0.8958786
## ENSMUSG00000026958 ENSMUSG00000026958 Dpp7 1.1117711
## ENSMUSG00000026311 ENSMUSG00000026311 Asb1 -0.4964109
## AveExpr F P.Value adj.P.Val
## ENSMUSG00000029816 7.143989 152.20167 2.012819e-13 3.549807e-09
## ENSMUSG00000024066 3.439929 77.96407 6.321700e-10 4.798971e-06
## ENSMUSG00000060429 7.109735 76.18836 8.163366e-10 4.798971e-06
## ENSMUSG00000028364 8.470727 68.27814 2.694219e-09 1.018236e-05
## ENSMUSG00000038244 6.373759 67.83940 2.886812e-09 1.018236e-05
## ENSMUSG00000041779 6.563752 61.07334 8.728055e-09 2.517510e-05
## ENSMUSG00000000171 6.919738 60.27925 9.992386e-09 2.517510e-05
## ENSMUSG00000022816 8.978962 59.37786 1.166804e-08 2.572220e-05
## ENSMUSG00000026958 5.100321 57.94348 1.498208e-08 2.759842e-05
## ENSMUSG00000026311 4.943539 57.69603 1.564891e-08 2.759842e-05results.SDC.time1 <- decideTests(fit.SDC.time1, adjust.method="BH")
summary(results.SDC.time1)## SDC.1d - con.1d
## -1 1536
## 0 15197
## 1 903write.fit(fit.SDC.time1, results=results.SDC.time1, file="SDC_time1.txt", digits=30, dec=",", adjust="BH")
CeO2.time4 <- makeContrasts(CeO2.4d-con.4d, levels=lev)
fit.CeO2.time4 <- contrasts.fit(fit, CeO2.time4)
fit.CeO2.time4 <- eBayes(fit.CeO2.time4)
fit.CeO2.time4$genes <- gene.list.retained
topTableF(fit.CeO2.time4, adjust="BH")## ensembl_gene_id external_gene_name CeO2.4d...con.4d
## ENSMUSG00000026185 ENSMUSG00000026185 Igfbp5 -1.2375330
## ENSMUSG00000029816 ENSMUSG00000029816 Gpnmb 1.4180214
## ENSMUSG00000029361 ENSMUSG00000029361 Nos1 1.3392718
## ENSMUSG00000047420 ENSMUSG00000047420 Fam180a 1.9153191
## ENSMUSG00000075602 ENSMUSG00000075602 Ly6a -1.2886489
## ENSMUSG00000028364 ENSMUSG00000028364 Tnc -1.1676646
## ENSMUSG00000039835 ENSMUSG00000039835 Nhsl1 0.7999249
## ENSMUSG00000032327 ENSMUSG00000032327 Stra6 1.6948127
## ENSMUSG00000055322 ENSMUSG00000055322 Tns1 1.3245553
## ENSMUSG00000027875 ENSMUSG00000027875 Hmgcs2 -0.8527799
## AveExpr F P.Value adj.P.Val
## ENSMUSG00000026185 6.848453 153.09284 1.867425e-13 3.293391e-09
## ENSMUSG00000029816 7.143989 85.35307 2.279191e-10 1.801199e-06
## ENSMUSG00000029361 3.753835 83.15893 3.063958e-10 1.801199e-06
## ENSMUSG00000047420 2.692762 77.45472 6.799763e-10 2.998016e-06
## ENSMUSG00000075602 5.739722 75.62301 8.863694e-10 3.126402e-06
## ENSMUSG00000028364 8.470727 68.99684 2.407714e-09 7.077074e-06
## ENSMUSG00000039835 6.680288 62.08685 7.356685e-09 1.452309e-05
## ENSMUSG00000032327 1.593701 61.80455 7.713940e-09 1.452309e-05
## ENSMUSG00000055322 4.542108 61.74802 7.787670e-09 1.452309e-05
## ENSMUSG00000027875 5.916811 61.41691 8.234913e-09 1.452309e-05results.CeO2.time4 <- decideTests(fit.CeO2.time4, adjust.method="BH")
summary(results.CeO2.time4)## CeO2.4d - con.4d
## -1 637
## 0 16324
## 1 675write.fit(fit.CeO2.time4, results=results.CeO2.time4, file="CeO2_time4.txt", digits=30, dec=",", adjust="BH")
NAC.time4 <- makeContrasts(NAC.4d-con.4d, levels=lev)
fit.NAC.time4 <- contrasts.fit(fit, NAC.time4)
fit.NAC.time4 <- eBayes(fit.NAC.time4)
fit.NAC.time4$genes <- gene.list.retained
topTableF(fit.NAC.time4, adjust="BH")## ensembl_gene_id external_gene_name NAC.4d...con.4d
## ENSMUSG00000019970 ENSMUSG00000019970 Sgk1 1.919480
## ENSMUSG00000019997 ENSMUSG00000019997 Ctgf 3.473345
## ENSMUSG00000028195 ENSMUSG00000028195 Cyr61 2.591405
## ENSMUSG00000026185 ENSMUSG00000026185 Igfbp5 -1.329619
## ENSMUSG00000024190 ENSMUSG00000024190 Dusp1 2.172764
## ENSMUSG00000038418 ENSMUSG00000038418 Egr1 2.839595
## ENSMUSG00000032501 ENSMUSG00000032501 Trib1 1.134671
## ENSMUSG00000024803 ENSMUSG00000024803 Ankrd1 1.499983
## ENSMUSG00000072915 ENSMUSG00000072915 Gm12258 -1.664447
## ENSMUSG00000019960 ENSMUSG00000019960 Dusp6 1.028233
## AveExpr F P.Value adj.P.Val
## ENSMUSG00000019970 6.431186 259.7780 1.619085e-16 2.175793e-12
## ENSMUSG00000019997 5.398320 251.9320 2.467445e-16 2.175793e-12
## ENSMUSG00000028195 8.003987 197.9644 6.440891e-15 3.786385e-11
## ENSMUSG00000026185 6.848453 177.0390 2.825845e-14 1.245915e-10
## ENSMUSG00000024190 5.248028 161.4538 9.403136e-14 3.316674e-10
## ENSMUSG00000038418 5.434777 144.3458 3.962395e-13 1.164680e-09
## ENSMUSG00000032501 4.650969 142.5572 4.642863e-13 1.169736e-09
## ENSMUSG00000024803 4.747288 126.3975 2.105038e-12 4.640556e-09
## ENSMUSG00000072915 2.632329 119.2282 4.331560e-12 8.487932e-09
## ENSMUSG00000019960 6.550829 98.3197 4.419086e-11 7.793501e-08results.NAC.time4 <- decideTests(fit.NAC.time4, adjust.method="BH")
summary(results.NAC.time4)## NAC.4d - con.4d
## -1 458
## 0 16720
## 1 458write.fit(fit.NAC.time4, results=results.NAC.time4, file="NAC_time4.txt", digits=30, dec=",", adjust="BH")
SDC.time4 <- makeContrasts(SDC.4d-con.4d, levels=lev)
fit.SDC.time4 <- contrasts.fit(fit, SDC.time4)
fit.SDC.time4 <- eBayes(fit.SDC.time4)
fit.SDC.time4$genes <- gene.list.retained
topTableF(fit.SDC.time4, adjust="BH")## ensembl_gene_id external_gene_name SDC.4d...con.4d
## ENSMUSG00000026185 ENSMUSG00000026185 Igfbp5 -1.2012457
## ENSMUSG00000047420 ENSMUSG00000047420 Fam180a 2.2186010
## ENSMUSG00000029361 ENSMUSG00000029361 Nos1 1.4739307
## ENSMUSG00000028364 ENSMUSG00000028364 Tnc -1.2887343
## ENSMUSG00000060477 ENSMUSG00000060477 Irak2 0.9106906
## ENSMUSG00000019929 ENSMUSG00000019929 Dcn 1.2589928
## ENSMUSG00000028195 ENSMUSG00000028195 Cyr61 1.5651711
## ENSMUSG00000072915 ENSMUSG00000072915 Gm12258 -1.1900383
## ENSMUSG00000026640 ENSMUSG00000026640 Plxna2 -0.7936002
## ENSMUSG00000039835 ENSMUSG00000039835 Nhsl1 0.8345112
## AveExpr F P.Value adj.P.Val
## ENSMUSG00000026185 6.848453 144.75169 3.823281e-13 6.742738e-09
## ENSMUSG00000047420 2.692762 108.82985 1.315740e-11 1.160219e-07
## ENSMUSG00000029361 3.753835 103.01549 2.541473e-11 1.494048e-07
## ENSMUSG00000028364 8.470727 84.06527 2.709566e-10 1.194647e-06
## ENSMUSG00000060477 3.838151 74.19291 1.093719e-09 3.857765e-06
## ENSMUSG00000019929 4.126106 71.67199 1.595721e-09 4.137101e-06
## ENSMUSG00000028195 8.003987 71.48341 1.642079e-09 4.137101e-06
## ENSMUSG00000072915 2.632329 68.85405 2.461943e-09 5.025928e-06
## ENSMUSG00000026640 6.841261 68.59210 2.564830e-09 5.025928e-06
## ENSMUSG00000039835 6.680288 67.85641 2.879080e-09 5.077545e-06results.SDC.time4 <- decideTests(fit.SDC.time4, adjust.method="BH")
summary(results.SDC.time4)## SDC.4d - con.4d
## -1 428
## 0 16756
## 1 452write.fit(fit.SDC.time4, results=results.SDC.time4, file="SDC_time4.txt", digits=30, dec=",", adjust="BH")
CeO2.time7 <- makeContrasts(CeO2.7d-con.7d, levels=lev)
fit.CeO2.time7 <- contrasts.fit(fit, CeO2.time7)
fit.CeO2.time7 <- eBayes(fit.CeO2.time7)
fit.CeO2.time7$genes <- gene.list.retained
topTableF(fit.CeO2.time7, adjust="BH")## ensembl_gene_id external_gene_name CeO2.7d...con.7d
## ENSMUSG00000069601 ENSMUSG00000069601 Ank3 -0.8563156
## ENSMUSG00000028364 ENSMUSG00000028364 Tnc -1.4072763
## ENSMUSG00000062093 ENSMUSG00000062093 Gm10110 -0.6439184
## ENSMUSG00000025355 ENSMUSG00000025355 Mmp19 -0.9604156
## ENSMUSG00000019929 ENSMUSG00000019929 Dcn 1.1793889
## ENSMUSG00000047420 ENSMUSG00000047420 Fam180a 1.1757364
## ENSMUSG00000044827 ENSMUSG00000044827 Tlr1 0.9157266
## ENSMUSG00000024593 ENSMUSG00000024593 Megf10 0.9051847
## ENSMUSG00000022103 ENSMUSG00000022103 Gfra2 -0.8624658
## ENSMUSG00000027544 ENSMUSG00000027544 Nfatc2 -1.1721159
## AveExpr F P.Value adj.P.Val
## ENSMUSG00000069601 7.176320 113.17541 8.189164e-12 1.444241e-07
## ENSMUSG00000028364 8.470727 103.87907 2.300560e-11 2.028633e-07
## ENSMUSG00000062093 8.266396 92.74484 8.756321e-11 3.375661e-07
## ENSMUSG00000025355 3.260961 92.24026 9.329734e-11 3.375661e-07
## ENSMUSG00000019929 4.126106 92.03828 9.570370e-11 3.375661e-07
## ENSMUSG00000047420 2.692762 89.04011 1.403774e-10 4.126161e-07
## ENSMUSG00000044827 1.500293 78.47352 5.879197e-10 1.481222e-06
## ENSMUSG00000024593 6.001670 74.76229 1.005561e-09 2.037275e-06
## ENSMUSG00000022103 4.596807 74.06462 1.114698e-09 2.037275e-06
## ENSMUSG00000027544 2.249053 73.26890 1.254775e-09 2.037275e-06results.CeO2.time7 <- decideTests(fit.CeO2.time7, adjust.method="BH")
summary(results.CeO2.time7)## CeO2.7d - con.7d
## -1 1424
## 0 14534
## 1 1678write.fit(fit.CeO2.time7, results=results.CeO2.time7, file="CeO2_time7.txt", digits=30, dec=",", adjust="BH")
NAC.time7 <- makeContrasts(NAC.7d-con.7d, levels=lev)
fit.NAC.time7 <- contrasts.fit(fit, NAC.time7)
fit.NAC.time7 <- eBayes(fit.NAC.time7)
fit.NAC.time7$genes <- gene.list.retained
topTableF(fit.NAC.time7, adjust="BH")## ensembl_gene_id external_gene_name NAC.7d...con.7d
## ENSMUSG00000069601 ENSMUSG00000069601 Ank3 -1.6438069
## ENSMUSG00000028364 ENSMUSG00000028364 Tnc -2.7128340
## ENSMUSG00000035493 ENSMUSG00000035493 Tgfbi -1.7221856
## ENSMUSG00000025355 ENSMUSG00000025355 Mmp19 -1.8424423
## ENSMUSG00000022144 ENSMUSG00000022144 Gdnf -1.4418602
## ENSMUSG00000020598 ENSMUSG00000020598 Nrcam -2.0745198
## ENSMUSG00000020303 ENSMUSG00000020303 Stc2 -0.9651392
## ENSMUSG00000023885 ENSMUSG00000023885 Thbs2 -1.8942438
## ENSMUSG00000082361 ENSMUSG00000082361 Btc -3.1310170
## ENSMUSG00000052942 ENSMUSG00000052942 Glis3 -1.2610950
## AveExpr F P.Value adj.P.Val
## ENSMUSG00000069601 7.1763201 411.4282 2.537724e-19 4.475529e-15
## ENSMUSG00000028364 8.4707270 383.0777 7.025819e-19 6.195367e-15
## ENSMUSG00000035493 7.9555511 332.5848 5.193061e-18 3.052827e-14
## ENSMUSG00000025355 3.2609609 299.0667 2.300523e-17 1.014301e-13
## ENSMUSG00000022144 4.3281149 220.3529 1.528402e-15 5.390980e-12
## ENSMUSG00000020598 2.9620820 210.3389 2.860459e-15 7.608347e-12
## ENSMUSG00000020303 6.1174329 209.4915 3.019870e-15 7.608347e-12
## ENSMUSG00000023885 2.3376063 198.7582 6.106105e-15 1.346091e-11
## ENSMUSG00000082361 0.5565074 181.8898 1.979978e-14 3.566890e-11
## ENSMUSG00000052942 4.9789029 181.5968 2.022505e-14 3.566890e-11results.NAC.time7 <- decideTests(fit.NAC.time7, adjust.method="BH")
summary(results.NAC.time7)## NAC.7d - con.7d
## -1 641
## 0 16323
## 1 672write.fit(fit.NAC.time7, results=results.NAC.time7, file="NAC_time7.txt", digits=30, dec=",", adjust="BH")
SDC.time7 <- makeContrasts(SDC.7d-con.7d, levels=lev)
fit.SDC.time7 <- contrasts.fit(fit, SDC.time7)
fit.SDC.time7 <- eBayes(fit.SDC.time7)
fit.SDC.time7$genes <- gene.list.retained
topTableF(fit.SDC.time7, adjust="BH")## ensembl_gene_id external_gene_name SDC.7d...con.7d
## ENSMUSG00000069601 ENSMUSG00000069601 Ank3 -1.3229839
## ENSMUSG00000028364 ENSMUSG00000028364 Tnc -2.0467524
## ENSMUSG00000025355 ENSMUSG00000025355 Mmp19 -1.3802758
## ENSMUSG00000035493 ENSMUSG00000035493 Tgfbi -1.0853308
## ENSMUSG00000082361 ENSMUSG00000082361 Btc -2.3005693
## ENSMUSG00000052942 ENSMUSG00000052942 Glis3 -1.0020587
## ENSMUSG00000038267 ENSMUSG00000038267 Slc22a23 -0.7826653
## ENSMUSG00000022144 ENSMUSG00000022144 Gdnf -1.0016806
## ENSMUSG00000062093 ENSMUSG00000062093 Gm10110 -0.6656981
## ENSMUSG00000020303 ENSMUSG00000020303 Stc2 -0.6403983
## AveExpr F P.Value adj.P.Val
## ENSMUSG00000069601 7.1763201 268.14720 1.045885e-16 1.844522e-12
## ENSMUSG00000028364 8.4707270 219.00283 1.660703e-15 1.464408e-11
## ENSMUSG00000025355 3.2609609 180.35935 2.213176e-14 1.301052e-10
## ENSMUSG00000035493 7.9555511 132.85588 1.129972e-12 4.982045e-09
## ENSMUSG00000082361 0.5565074 129.60977 1.539919e-12 5.431603e-09
## ENSMUSG00000052942 4.9789029 117.26623 5.309398e-12 1.560609e-08
## ENSMUSG00000038267 6.5631790 113.46837 7.935668e-12 1.754351e-08
## ENSMUSG00000022144 4.3281149 113.44212 7.958043e-12 1.754351e-08
## ENSMUSG00000062093 8.2663964 99.15558 3.998767e-11 7.835806e-08
## ENSMUSG00000020303 6.1174329 93.30228 8.166203e-11 1.440192e-07results.SDC.time7 <- decideTests(fit.SDC.time7, adjust.method="BH")
summary(results.SDC.time7)## SDC.7d - con.7d
## -1 360
## 0 16986
## 1 290write.fit(fit.SDC.time7, results=results.SDC.time7, file="SDC_time7.txt", digits=30, dec=",", adjust="BH")
save(list=ls(pattern = "fit"), file = "FitLM.rdata")
NAC.CeO2.time1 <- makeContrasts(CeO2.1d-NAC.1d, levels=lev)
fit.NAC.CeO2.time1 <- contrasts.fit(fit, NAC.CeO2.time1)
fit.NAC.CeO2.time1 <- eBayes(fit.NAC.CeO2.time1)
fit.NAC.CeO2.time1$genes <- gene.list.retained
topTableF(fit.NAC.CeO2.time1, adjust="BH")## ensembl_gene_id external_gene_name CeO2.1d...NAC.1d
## ENSMUSG00000023832 ENSMUSG00000023832 Acat2 1.4008095
## ENSMUSG00000024661 ENSMUSG00000024661 Fth1 1.1391337
## ENSMUSG00000021252 ENSMUSG00000021252 0610007P14Rik 1.0144503
## ENSMUSG00000021273 ENSMUSG00000021273 Fdft1 0.9884982
## ENSMUSG00000060429 ENSMUSG00000060429 Sntb1 -1.1895586
## ENSMUSG00000040152 ENSMUSG00000040152 Thbs1 -1.7398227
## ENSMUSG00000034573 ENSMUSG00000034573 Ptpn13 -1.1246153
## ENSMUSG00000028124 ENSMUSG00000028124 Gclm 1.2248098
## ENSMUSG00000020032 ENSMUSG00000020032 Nuak1 -1.2320931
## ENSMUSG00000019326 ENSMUSG00000019326 Aoc3 -2.1139132
## AveExpr F P.Value adj.P.Val
## ENSMUSG00000023832 7.684751 222.9379 1.305404e-15 2.302210e-11
## ENSMUSG00000024661 9.452124 187.6886 1.307894e-14 8.202750e-11
## ENSMUSG00000021252 5.896574 186.7731 1.395342e-14 8.202750e-11
## ENSMUSG00000021273 7.032517 177.6601 2.698767e-14 1.189887e-10
## ENSMUSG00000060429 7.109735 170.8611 4.500284e-14 1.587340e-10
## ENSMUSG00000040152 8.312672 167.6707 5.755173e-14 1.691637e-10
## ENSMUSG00000034573 5.450616 165.2151 6.973681e-14 1.756969e-10
## ENSMUSG00000028124 6.175399 161.2263 9.576507e-14 2.111141e-10
## ENSMUSG00000020032 5.442616 158.6327 1.181210e-13 2.115615e-10
## ENSMUSG00000019326 3.661587 158.1183 1.231828e-13 2.115615e-10results.NAC.CeO2.time1 <- decideTests(fit.NAC.CeO2.time1, adjust.method="BH")
summary(results.NAC.CeO2.time1)## CeO2.1d - NAC.1d
## -1 4082
## 0 9725
## 1 3829write.fit(fit.NAC.CeO2.time1, results=results.NAC.CeO2.time1, file="CeO2_NAC_time1.txt", digits=30, dec=",", adjust="BH")
NAC.CeO2.time4 <- makeContrasts(CeO2.4d-NAC.4d, levels=lev)
fit.NAC.CeO2.time4 <- contrasts.fit(fit, NAC.CeO2.time4)
fit.NAC.CeO2.time4 <- eBayes(fit.NAC.CeO2.time4)
fit.NAC.CeO2.time4$genes <- gene.list.retained
topTableF(fit.NAC.CeO2.time4, adjust="BH")## ensembl_gene_id external_gene_name CeO2.4d...NAC.4d
## ENSMUSG00000019997 ENSMUSG00000019997 Ctgf -2.6655824
## ENSMUSG00000019970 ENSMUSG00000019970 Sgk1 -1.3093063
## ENSMUSG00000029816 ENSMUSG00000029816 Gpnmb 1.6361749
## ENSMUSG00000032501 ENSMUSG00000032501 Trib1 -0.9847253
## ENSMUSG00000024190 ENSMUSG00000024190 Dusp1 -1.5677053
## ENSMUSG00000032327 ENSMUSG00000032327 Stra6 2.0140085
## ENSMUSG00000024803 ENSMUSG00000024803 Ankrd1 -1.1826516
## ENSMUSG00000026475 ENSMUSG00000026475 Rgs16 -1.0966683
## ENSMUSG00000028195 ENSMUSG00000028195 Cyr61 -1.6163896
## ENSMUSG00000022055 ENSMUSG00000022055 Nefl -1.0749928
## AveExpr F P.Value adj.P.Val
## ENSMUSG00000019997 5.398320 179.42186 2.370339e-14 4.180330e-10
## ENSMUSG00000019970 6.431186 128.82292 1.661488e-12 1.465100e-08
## ENSMUSG00000029816 7.143989 113.60244 7.822462e-12 4.598565e-08
## ENSMUSG00000032501 4.650969 110.87912 1.050176e-11 4.630224e-08
## ENSMUSG00000024190 5.248028 93.31820 8.149985e-11 2.874663e-07
## ENSMUSG00000032327 1.593701 84.25317 2.641717e-10 7.305652e-07
## ENSMUSG00000024803 4.747288 83.56424 2.899726e-10 7.305652e-07
## ENSMUSG00000026475 5.247709 79.45705 5.115585e-10 1.062916e-06
## ENSMUSG00000028195 8.003987 79.04176 5.424269e-10 1.062916e-06
## ENSMUSG00000022055 5.453674 74.67030 1.019274e-09 1.797592e-06results.NAC.CeO2.time4 <- decideTests(fit.NAC.CeO2.time4, adjust.method="BH")
summary(results.NAC.CeO2.time4)## CeO2.4d - NAC.4d
## -1 190
## 0 17260
## 1 186write.fit(fit.NAC.CeO2.time4, results=results.NAC.CeO2.time4, file="CeO2_NAC_time4.txt", digits=30, dec=",", adjust="BH")
NAC.CeO2.time7 <- makeContrasts(CeO2.7d-NAC.7d, levels=lev)
fit.NAC.CeO2.time7 <- contrasts.fit(fit, NAC.CeO2.time7)
fit.NAC.CeO2.time7 <- eBayes(fit.NAC.CeO2.time7)
fit.NAC.CeO2.time7$genes <- gene.list.retained
topTableF(fit.NAC.CeO2.time7, adjust="BH")## ensembl_gene_id external_gene_name CeO2.7d...NAC.7d
## ENSMUSG00000023885 ENSMUSG00000023885 Thbs2 1.8580065
## ENSMUSG00000031375 ENSMUSG00000031375 Bgn 1.2619047
## ENSMUSG00000020908 ENSMUSG00000020908 Myh3 -1.3781729
## ENSMUSG00000057123 ENSMUSG00000057123 Gja5 1.4133559
## ENSMUSG00000028195 ENSMUSG00000028195 Cyr61 -2.1102636
## ENSMUSG00000019838 ENSMUSG00000019838 Slc16a10 1.1838027
## ENSMUSG00000022144 ENSMUSG00000022144 Gdnf 1.0827056
## ENSMUSG00000055368 ENSMUSG00000055368 Slc6a2 1.2659772
## ENSMUSG00000020598 ENSMUSG00000020598 Nrcam 1.5526576
## ENSMUSG00000035493 ENSMUSG00000035493 Tgfbi 0.9762928
## AveExpr F P.Value adj.P.Val
## ENSMUSG00000023885 2.337606 188.3031 1.252479e-14 2.208872e-10
## ENSMUSG00000031375 5.332354 161.0312 9.727916e-14 8.578076e-10
## ENSMUSG00000020908 2.631798 134.3107 9.855738e-13 5.248750e-09
## ENSMUSG00000057123 1.090752 131.3886 1.298661e-12 5.248750e-09
## ENSMUSG00000028195 8.003987 129.9657 1.488079e-12 5.248750e-09
## ENSMUSG00000019838 4.058191 119.9650 4.015557e-12 1.030485e-08
## ENSMUSG00000022144 4.328115 119.7857 4.090153e-12 1.030485e-08
## ENSMUSG00000055368 1.013349 116.3488 5.845064e-12 1.288544e-08
## ENSMUSG00000020598 2.962082 112.5452 8.764206e-12 1.717395e-08
## ENSMUSG00000035493 7.955551 106.2987 1.746329e-11 3.079826e-08results.NAC.CeO2.time7 <- decideTests(fit.NAC.CeO2.time7, adjust.method="BH")
summary(results.NAC.CeO2.time7)## CeO2.7d - NAC.7d
## -1 1158
## 0 14531
## 1 1947write.fit(fit.NAC.CeO2.time7, results=results.NAC.CeO2.time7, file="CeO2_NAC_time7.txt", digits=30, dec=",", adjust="BH")
NAC.SDC.time1 <- makeContrasts(SDC.1d-NAC.1d, levels=lev)
fit.NAC.SDC.time1 <- contrasts.fit(fit, NAC.SDC.time1)
fit.NAC.SDC.time1 <- eBayes(fit.NAC.SDC.time1)
fit.NAC.SDC.time1$genes <- gene.list.retained
topTableF(fit.NAC.SDC.time1, adjust="BH")## ensembl_gene_id external_gene_name SDC.1d...NAC.1d
## ENSMUSG00000040152 ENSMUSG00000040152 Thbs1 -1.935494
## ENSMUSG00000019326 ENSMUSG00000019326 Aoc3 -2.271926
## ENSMUSG00000029185 ENSMUSG00000029185 Fam114a1 -1.259586
## ENSMUSG00000021367 ENSMUSG00000021367 Edn1 -2.398189
## ENSMUSG00000025610 ENSMUSG00000025610 Map3k7cl -1.927991
## ENSMUSG00000019997 ENSMUSG00000019997 Ctgf -2.144280
## ENSMUSG00000029816 ENSMUSG00000029816 Gpnmb 1.929917
## ENSMUSG00000032232 ENSMUSG00000032232 Cgnl1 -1.328018
## ENSMUSG00000020053 ENSMUSG00000020053 Igf1 -2.122750
## ENSMUSG00000022816 ENSMUSG00000022816 Fstl1 -1.430177
## AveExpr F P.Value adj.P.Val
## ENSMUSG00000040152 8.312672 207.4235 3.450017e-15 6.084451e-11
## ENSMUSG00000019326 3.661587 182.9057 1.839736e-14 1.227471e-10
## ENSMUSG00000029185 6.261504 181.1582 2.088009e-14 1.227471e-10
## ENSMUSG00000021367 1.941905 170.6111 4.587193e-14 2.022493e-10
## ENSMUSG00000025610 1.879207 161.3432 9.487021e-14 3.134377e-10
## ENSMUSG00000019997 5.398320 159.3601 1.113390e-13 3.134377e-10
## ENSMUSG00000029816 7.143989 156.7269 1.380667e-13 3.134377e-10
## ENSMUSG00000032232 6.089785 155.0914 1.580497e-13 3.134377e-10
## ENSMUSG00000020053 4.676236 154.9473 1.599535e-13 3.134377e-10
## ENSMUSG00000022816 8.978962 152.4747 1.967039e-13 3.469070e-10results.NAC.SDC.time1 <- decideTests(fit.NAC.SDC.time1, adjust.method="BH")
summary(results.NAC.SDC.time1)## SDC.1d - NAC.1d
## -1 2063
## 0 14084
## 1 1489write.fit(fit.NAC.SDC.time1, results=results.NAC.SDC.time1, file="SDC_NAC_time1.txt", digits=30, dec=",", adjust="BH")
NAC.SDC.time4 <- makeContrasts(SDC.4d-NAC.4d, levels=lev)
fit.NAC.SDC.time4 <- contrasts.fit(fit, NAC.SDC.time4)
fit.NAC.SDC.time4 <- eBayes(fit.NAC.SDC.time4)
fit.NAC.SDC.time4$genes <- gene.list.retained
topTableF(fit.NAC.SDC.time4, adjust="BH")## ensembl_gene_id external_gene_name SDC.4d...NAC.4d
## ENSMUSG00000057123 ENSMUSG00000057123 Gja5 1.6699868
## ENSMUSG00000026475 ENSMUSG00000026475 Rgs16 -1.2001682
## ENSMUSG00000029361 ENSMUSG00000029361 Nos1 1.3567787
## ENSMUSG00000035296 ENSMUSG00000035296 Sgcg 1.5552771
## ENSMUSG00000023885 ENSMUSG00000023885 Thbs2 1.5271173
## ENSMUSG00000029816 ENSMUSG00000029816 Gpnmb 1.4362113
## ENSMUSG00000032501 ENSMUSG00000032501 Trib1 -0.8336082
## ENSMUSG00000019997 ENSMUSG00000019997 Ctgf -1.6558485
## ENSMUSG00000022054 ENSMUSG00000022054 Nefm -1.2006945
## ENSMUSG00000030894 ENSMUSG00000030894 Tpp1 0.5667378
## AveExpr F P.Value adj.P.Val
## ENSMUSG00000057123 1.0907521 95.57332 6.165669e-11 3.994541e-07
## ENSMUSG00000026475 5.2477091 95.53614 6.193846e-11 3.994541e-07
## ENSMUSG00000029361 3.7538349 93.19464 8.276759e-11 3.994541e-07
## ENSMUSG00000035296 0.7830585 92.47340 9.059971e-11 3.994541e-07
## ENSMUSG00000023885 2.3376063 90.61494 1.146543e-10 4.044085e-07
## ENSMUSG00000029816 7.1439894 87.42811 1.731816e-10 5.090386e-07
## ENSMUSG00000032501 4.6509686 83.41111 2.960646e-10 7.331798e-07
## ENSMUSG00000019997 5.3983203 82.55825 3.325833e-10 7.331798e-07
## ENSMUSG00000022054 5.4875950 79.46646 5.108813e-10 1.001100e-06
## ENSMUSG00000030894 6.5169718 72.22096 1.468536e-09 2.589909e-06results.NAC.SDC.time4 <- decideTests(fit.NAC.SDC.time4, adjust.method="BH")
summary(results.NAC.SDC.time4)## SDC.4d - NAC.4d
## -1 227
## 0 17132
## 1 277write.fit(fit.NAC.SDC.time4, results=results.NAC.SDC.time4, file="SDC_NAC_time4.txt", digits=30, dec=",", adjust="BH")
NAC.SDC.time7 <- makeContrasts(SDC.7d-NAC.7d, levels=lev)
fit.NAC.SDC.time7 <- contrasts.fit(fit, NAC.SDC.time7)
fit.NAC.SDC.time7 <- eBayes(fit.NAC.SDC.time7)
fit.NAC.SDC.time7$genes <- gene.list.retained
topTableF(fit.NAC.SDC.time7, adjust="BH")## ensembl_gene_id external_gene_name SDC.7d...NAC.7d
## ENSMUSG00000031375 ENSMUSG00000031375 Bgn 1.5651928
## ENSMUSG00000023885 ENSMUSG00000023885 Thbs2 2.0987393
## ENSMUSG00000042436 ENSMUSG00000042436 Mfap4 1.7258001
## ENSMUSG00000057123 ENSMUSG00000057123 Gja5 1.2123181
## ENSMUSG00000028463 ENSMUSG00000028463 Car9 3.5966229
## ENSMUSG00000055368 ENSMUSG00000055368 Slc6a2 1.0739026
## ENSMUSG00000026185 ENSMUSG00000026185 Igfbp5 0.8121469
## ENSMUSG00000035105 ENSMUSG00000035105 Egln3 1.4714376
## ENSMUSG00000026051 ENSMUSG00000026051 1500015O10Rik 1.0080688
## ENSMUSG00000066438 ENSMUSG00000066438 Plekhd1 1.6022431
## AveExpr F P.Value adj.P.Val
## ENSMUSG00000031375 5.3323542 248.78381 2.931594e-16 2.724074e-12
## ENSMUSG00000023885 2.3376063 247.83424 3.089220e-16 2.724074e-12
## ENSMUSG00000042436 2.2263075 179.64311 2.332206e-14 1.371026e-10
## ENSMUSG00000057123 1.0907521 94.58944 6.959474e-11 3.068432e-07
## ENSMUSG00000028463 1.7148680 82.75973 3.235433e-10 1.046429e-06
## ENSMUSG00000055368 1.0133489 82.06217 3.560088e-10 1.046429e-06
## ENSMUSG00000026185 6.8484527 66.90860 3.345701e-09 8.429255e-06
## ENSMUSG00000035105 3.4577011 65.07423 4.493602e-09 9.906146e-06
## ENSMUSG00000026051 0.7618651 60.30077 9.955659e-09 1.809296e-05
## ENSMUSG00000066438 -1.4509850 60.12544 1.025911e-08 1.809296e-05results.NAC.SDC.time7 <- decideTests(fit.NAC.SDC.time7, adjust.method="BH")
summary(results.NAC.SDC.time7)## SDC.7d - NAC.7d
## -1 142
## 0 17283
## 1 211write.fit(fit.NAC.SDC.time7, results=results.NAC.SDC.time7, file="SDC_NAC_time7.txt", digits=30, dec=",", adjust="BH")
#save(list=ls(pattern = "fit."), file = "FitLM.rdata")Additional contrasts
load("FitLM.rdata")
CeO2.SDC.time1 <- makeContrasts(CeO2.1d-SDC.1d, levels=lev)
fit.CeO2.SDC.time1 <- contrasts.fit(fit, CeO2.SDC.time1)
fit.CeO2.SDC.time1 <- eBayes(fit.CeO2.SDC.time1)
fit.CeO2.SDC.time1$genes <- gene.list.retained
topTableF(fit.CeO2.SDC.time1, adjust="BH")## ensembl_gene_id external_gene_name CeO2.1d...SDC.1d
## ENSMUSG00000090290 ENSMUSG00000090290 Gm17296 -0.5991897
## ENSMUSG00000020225 ENSMUSG00000020225 Tmbim4 0.6388168
## ENSMUSG00000018567 ENSMUSG00000018567 Gabarap 0.6338241
## ENSMUSG00000001962 ENSMUSG00000001962 Fam50a 0.5210134
## ENSMUSG00000008450 ENSMUSG00000008450 Nutf2 0.4758870
## ENSMUSG00000038872 ENSMUSG00000038872 Zfhx3 0.5392008
## ENSMUSG00000095762 ENSMUSG00000095762 Gm16378 0.7333790
## ENSMUSG00000021665 ENSMUSG00000021665 Hexb 0.6931579
## ENSMUSG00000049775 ENSMUSG00000049775 Tmsb4x 0.6060597
## ENSMUSG00000027637 ENSMUSG00000027637 1110008F13Rik 0.5524029
## AveExpr F P.Value adj.P.Val
## ENSMUSG00000090290 5.134911 60.71726 9.272523e-09 0.0001635302
## ENSMUSG00000020225 5.743039 52.58805 3.958089e-08 0.0003256372
## ENSMUSG00000018567 8.071717 48.98737 7.890719e-08 0.0003256372
## ENSMUSG00000001962 5.610451 48.44746 8.774913e-08 0.0003256372
## ENSMUSG00000008450 4.971014 48.19056 9.232172e-08 0.0003256372
## ENSMUSG00000038872 5.623087 42.68668 2.861762e-07 0.0008411673
## ENSMUSG00000095762 4.435585 39.12365 6.244207e-07 0.0013228021
## ENSMUSG00000021665 5.871995 38.96044 6.477766e-07 0.0013228021
## ENSMUSG00000049775 8.223789 38.13273 7.814644e-07 0.0013228021
## ENSMUSG00000027637 5.913427 38.06286 7.940250e-07 0.0013228021results.CeO2.SDC.time1 <- decideTests(fit.CeO2.SDC.time1, adjust.method="BH")
summary(results.CeO2.SDC.time1)## CeO2.1d - SDC.1d
## -1 3262
## 0 10635
## 1 3739write.fit(fit.CeO2.SDC.time1, results=results.CeO2.SDC.time1, file="CeO2_SDC_time1.txt", digits=30, dec=",", adjust="BH")
CeO2.SDC.time4 <- makeContrasts(CeO2.4d-SDC.4d, levels=lev)
fit.CeO2.SDC.time4 <- contrasts.fit(fit, CeO2.SDC.time4)
fit.CeO2.SDC.time4 <- eBayes(fit.CeO2.SDC.time4)
fit.CeO2.SDC.time4$genes <- gene.list.retained
topTableF(fit.CeO2.SDC.time4, adjust="BH")## ensembl_gene_id external_gene_name CeO2.4d...SDC.4d
## ENSMUSG00000019997 ENSMUSG00000019997 Ctgf -1.0097339
## ENSMUSG00000085148 ENSMUSG00000085148 Mir22hg -0.4976070
## ENSMUSG00000025993 ENSMUSG00000025993 Slc40a1 -0.5270368
## ENSMUSG00000026981 ENSMUSG00000026981 Il1rn -2.8818822
## ENSMUSG00000092730 ENSMUSG00000092730 Snora24 0.8733184
## ENSMUSG00000097367 ENSMUSG00000097367 Gm26718 -2.1988837
## ENSMUSG00000037708 ENSMUSG00000037708 BC061194 1.5414872
## ENSMUSG00000073652 ENSMUSG00000073652 Apol7d -1.7585741
## ENSMUSG00000074037 ENSMUSG00000074037 Mc1r 1.2012258
## ENSMUSG00000084799 ENSMUSG00000084799 Ino80dos -0.8027072
## AveExpr F P.Value adj.P.Val
## ENSMUSG00000019997 5.3983203 23.75303 3.163934e-05 0.5579914
## ENSMUSG00000085148 4.9384089 20.63403 8.105370e-05 0.6738262
## ENSMUSG00000025993 4.6973869 18.11343 1.816820e-04 0.6738262
## ENSMUSG00000026981 -3.0811540 14.63507 5.995618e-04 0.6738262
## ENSMUSG00000092730 1.3438638 14.20432 7.001645e-04 0.6738262
## ENSMUSG00000097367 -3.0884924 13.36716 9.512771e-04 0.6738262
## ENSMUSG00000037708 -1.6181927 13.30774 9.724505e-04 0.6738262
## ENSMUSG00000073652 -1.1852883 13.28449 9.808722e-04 0.6738262
## ENSMUSG00000074037 -0.9828242 12.96098 1.106539e-03 0.6738262
## ENSMUSG00000084799 0.7951925 12.69374 1.223379e-03 0.6738262results.CeO2.SDC.time4 <- decideTests(fit.CeO2.SDC.time4, adjust.method="BH")
summary(results.CeO2.SDC.time4)## CeO2.4d - SDC.4d
## -1 0
## 0 17636
## 1 0write.fit(fit.CeO2.SDC.time4, results=results.CeO2.SDC.time4, file="CeO2_SDC_time4.txt", digits=30, dec=",", adjust="BH")
CeO2.SDC.time7 <- makeContrasts(CeO2.7d-SDC.7d, levels=lev)
fit.CeO2.SDC.time7 <- contrasts.fit(fit, CeO2.SDC.time7)
fit.CeO2.SDC.time7 <- eBayes(fit.CeO2.SDC.time7)
fit.CeO2.SDC.time7$genes <- gene.list.retained
topTableF(fit.CeO2.SDC.time7, adjust="BH")## ensembl_gene_id external_gene_name CeO2.7d...SDC.7d
## ENSMUSG00000022144 ENSMUSG00000022144 Gdnf 0.6425260
## ENSMUSG00000047085 ENSMUSG00000047085 Lrrc4b -3.7657933
## ENSMUSG00000028195 ENSMUSG00000028195 Cyr61 -1.1586725
## ENSMUSG00000042436 ENSMUSG00000042436 Mfap4 -0.7432573
## ENSMUSG00000038418 ENSMUSG00000038418 Egr1 -1.3920735
## ENSMUSG00000069601 ENSMUSG00000069601 Ank3 0.4666683
## ENSMUSG00000039153 ENSMUSG00000039153 Runx2 0.5258922
## ENSMUSG00000028463 ENSMUSG00000028463 Car9 -1.6122378
## ENSMUSG00000058254 ENSMUSG00000058254 Tspan7 -0.5146937
## ENSMUSG00000007097 ENSMUSG00000007097 Atp1a2 -0.7743870
## AveExpr F P.Value adj.P.Val
## ENSMUSG00000022144 4.328115 44.89204 1.800264e-07 0.002275240
## ENSMUSG00000047085 -3.683797 43.17359 2.580222e-07 0.002275240
## ENSMUSG00000028195 8.003987 38.67586 6.907594e-07 0.004060744
## ENSMUSG00000042436 2.226307 36.71628 1.083293e-06 0.004776240
## ENSMUSG00000038418 5.434777 34.07476 2.031253e-06 0.007164636
## ENSMUSG00000069601 7.176320 32.98473 2.653623e-06 0.007799882
## ENSMUSG00000039153 6.038302 31.44540 3.902656e-06 0.009832464
## ENSMUSG00000028463 1.714868 29.95679 5.722300e-06 0.012614811
## ENSMUSG00000058254 4.863332 29.45541 6.524151e-06 0.012784437
## ENSMUSG00000007097 3.622022 28.09422 9.369448e-06 0.016523959results.CeO2.SDC.time7 <- decideTests(fit.CeO2.SDC.time7, adjust.method="BH")
summary(results.CeO2.SDC.time7)## CeO2.7d - SDC.7d
## -1 57
## 0 17541
## 1 38write.fit(fit.CeO2.SDC.time7, results=results.CeO2.SDC.time7, file="CeO2_SDC_time7.txt", digits=30, dec=",", adjust="BH")