The nested interactions study design successfully isolates the genes that are differentially expressed in the mutant strain (GFR) vs. the control strain (GF). However, there is a key decision to be made: How to decide to filter the list of DE genes? There does not seem to be a single method used in the literature. The method applied has a very large consequence regarding how large the DE gene list is and therefore which pathways are concluded to be affected. This ranges from a single gene to hundreds. This document will apply four example DE filters for demonstration purposes. To aid interpretation, over-representation analysis (pathways and GO modules) is performed on the resulting DE list (via http://cpdb.molgen.mpg.de/)
Filtering methods include:
Annotation <- read.csv("HTA-2_0.na35.2.hg19.transcript.csv/HTA-2_0.na35.2.hg19.transcript.csv", header=TRUE, skip=19)
probe.gene.map <- read.csv("probe.gene.map.csv")metadata and .CEL files are imported and the test matrix is prepared
targets <- read.csv("targets.txt", as.is=T)
Experiment <- factor(targets$Experiment)
Strain <- factor(targets$Strain, levels=c("GF","GFR"))
Treatment <- factor(targets$Treatment, levels=c("control","drug"))
dat <- read.celfiles(targets$FileName)## Reading in : 20160505_HTA2.0_0316_WTH_1R_(HTA-2_0).CEL
## Reading in : 20160505_HTA2.0_0317_WTH_2R_(HTA-2_0).CEL
## Reading in : 20160505_HTA2.0_0318_WTH_3R_(HTA-2_0).CEL
## Reading in : 20160505_HTA2.0_0319_WTH_4R_(HTA-2_0).CEL
## Reading in : 20160616_HTA2.0_0333_WTH_1_R1_(HTA-2_0).CEL
## Reading in : 20160616_HTA2.0_0334_WTH_2_R1_(HTA-2_0).CEL
## Reading in : 20160616_HTA2.0_0335_WTH_3_R2_(HTA-2_0).CEL
## Reading in : 20160616_HTA2.0_0336_WTH_4_R1_(HTA-2_0).CELproject.bgcorrect.norm.avg <- rma(dat, background=TRUE, normalize=TRUE)## Background correcting
## Normalizing
## Calculating Expressionproject.bgcorrect.norm.avg.filt <- exprs(project.bgcorrect.norm.avg)[which(rownames(project.bgcorrect.norm.avg) %in% Annotation[,1]),]
design2 <- model.matrix(~Experiment+Strain+Strain:Treatment)eset <- project.bgcorrect.norm.avg.filt
fit <- lmFit(eset, design2)
fit <- eBayes(fit, trend=T, robust=T)
fit2 <- contrasts.fit(fit, c(0,0,0,-1,1))
fit2 <- eBayes(fit2)
diff.tGFR <- topTable(fit2, p.value=.05,number=Inf)
diff.tGFR <- setDT(diff.tGFR, keep.rownames = TRUE)[]
colnames(diff.tGFR)[1] <- "probe"
diff.tGFR <- dplyr::left_join(diff.tGFR,probe.gene.map,by="probe")
diff.tGFR.size <- diff.tGFR[order(-diff.tGFR$logFC),]
write.csv(diff.tGFR, "DE_filtering_testing/strict.fdr.csv")
kable(diff.tGFR.size) %>%
kable_styling() %>%
scroll_box(width = "100%", height = "400px")| probe | logFC | AveExpr | t | P.Value | adj.P.Val | B | name | description | |
|---|---|---|---|---|---|---|---|---|---|
| 1 | TC6_dbb_hap3000083.hg.1 | 1.736426 | 4.021221 | 11.87276 | 2.4e-06 | 0.0436953 | -2.977216 | HLA-DRA | major histocompatibility complex, class II, DR alpha |
| 6 | TC6_mann_hap4000074.hg.1 | 1.669528 | 4.118256 | 11.22123 | 3.7e-06 | 0.0436953 | -2.991608 | HLA-DRA | major histocompatibility complex, class II, DR alpha |
| 3 | TC6_mcf_hap5000075.hg.1 | 1.664986 | 4.117026 | 11.24342 | 3.7e-06 | 0.0436953 | -2.991081 | HLA-DRA | major histocompatibility complex, class II, DR alpha |
| 4 | TC6_qbl_hap6000081.hg.1 | 1.664986 | 4.117026 | 11.24342 | 3.7e-06 | 0.0436953 | -2.991081 | HLA-DRA | major histocompatibility complex, class II, DR alpha |
| 5 | TC6_ssto_hap7000076.hg.1 | 1.664986 | 4.117026 | 11.24342 | 3.7e-06 | 0.0436953 | -2.991081 | HLA-DRA | major histocompatibility complex, class II, DR alpha |
| 2 | TC06000399.hg.1 | 1.660262 | 3.999679 | 11.28636 | 3.6e-06 | 0.0436953 | -2.990068 | HLA-DRA | major histocompatibility complex, class II, DR alpha |
This strict method allows only six probes through, all of which map to the same gene (HLA-DRA). Over-representation analysis is not possible with only one gene! HLA-DRA maps to 54 different pathways! While this is very confident, it leaves us having to be purely speculative as to interpretation.
eset <- project.bgcorrect.norm.avg.filt
fit <- lmFit(eset, design2)
fit <- eBayes(fit, trend=T, robust=T)
fit2 <- contrasts.fit(fit, c(0,0,0,-1,1))
fit2 <- eBayes(fit2)
diff.tGFR <- topTable(fit2, p.value=.005, adjust.method = "none", number=Inf)
diff.tGFR <- setDT(diff.tGFR, keep.rownames = TRUE)[]
colnames(diff.tGFR)[1] <- "probe"
diff.tGFR <- dplyr::left_join(diff.tGFR,probe.gene.map,by="probe")
diff.tGFR.size <- diff.tGFR[order(-abs(diff.tGFR$logFC)),]
write.csv(diff.tGFR, "DE_filtering_testing/nonadjusted.pvalue.csv")
kable(diff.tGFR.size) %>%
kable_styling() %>%
scroll_box(width = "100%", height = "400px")| probe | logFC | AveExpr | t | P.Value | adj.P.Val | B | name | description | |
|---|---|---|---|---|---|---|---|---|---|
| 10 | 3597981_st | -3.6560418 | 1.951490 | -7.830909 | 0.0000524 | 0.0000524 | -3.122281 | — | — |
| 216 | TC10002568.hg.1 | 2.6618371 | 5.316601 | 4.009678 | 0.0039380 | 0.0039380 | -3.598487 | — | — |
| 219 | TC10002567.hg.1 | 2.5639951 | 3.893117 | 3.997068 | 0.0040077 | 0.0040077 | -3.601404 | — | — |
| 8 | 47424360_st | 2.4762003 | 2.704951 | 8.838574 | 0.0000219 | 0.0000219 | -3.069890 | — | — |
| 86 | TC01005754.hg.1 | 2.3954102 | 6.144722 | 4.872871 | 0.0012538 | 0.0012538 | -3.427984 | — | — |
| 27 | 2985876_st | 2.3472452 | 5.731316 | 5.646420 | 0.0004925 | 0.0004925 | -3.315305 | — | — |
| 192 | TC04000408.hg.1 | 2.1968195 | 3.856812 | 4.114278 | 0.0034081 | 0.0034081 | -3.574803 | CXCL8 | chemokine (C-X-C motif) ligand 8 |
| 39 | TC08001612.hg.1 | 2.1968151 | 3.636100 | 5.406042 | 0.0006526 | 0.0006526 | -3.346958 | — | — |
| 152 | 47424061_st | 2.1814129 | 2.169571 | 4.311166 | 0.0026077 | 0.0026077 | -3.532630 | — | — |
| 48 | TC01005830.hg.1 | -2.0246084 | 4.657497 | -5.219109 | 0.0008168 | 0.0008168 | -3.373569 | FLG | filaggrin |
| 193 | TC02001364.hg.1 | 2.0166611 | 2.975513 | 4.103289 | 0.0034599 | 0.0034599 | -3.577249 | CCL20 | chemokine (C-C motif) ligand 20 |
| 38 | 47424232_st | -1.8411164 | 1.776524 | -5.445155 | 0.0006230 | 0.0006230 | -3.341617 | — | — |
| 213 | 47421298_st | 1.8389215 | 2.238743 | 4.024874 | 0.0038558 | 0.0038558 | -3.594990 | — | — |
| 52 | TC15000024.hg.1 | 1.8246391 | 4.616064 | 5.159258 | 0.0008785 | 0.0008785 | -3.382484 | — | — |
| 53 | TC15000148.hg.1 | 1.8246391 | 4.616064 | 5.159258 | 0.0008785 | 0.0008785 | -3.382484 | — | — |
| 54 | TC15000207.hg.1 | 1.8246391 | 4.616064 | 5.159258 | 0.0008785 | 0.0008785 | -3.382484 | — | — |
| 55 | TC15000238.hg.1 | 1.8246391 | 4.616064 | 5.159258 | 0.0008785 | 0.0008785 | -3.382484 | — | — |
| 56 | TC15000243.hg.1 | 1.8246391 | 4.616064 | 5.159258 | 0.0008785 | 0.0008785 | -3.382484 | — | — |
| 57 | TC15001014.hg.1 | 1.8246391 | 4.616064 | 5.159258 | 0.0008785 | 0.0008785 | -3.382484 | — | — |
| 58 | TC15001053.hg.1 | 1.8246391 | 4.616064 | 5.159258 | 0.0008785 | 0.0008785 | -3.382484 | — | — |
| 59 | TC15001115.hg.1 | 1.8246391 | 4.616064 | 5.159258 | 0.0008785 | 0.0008785 | -3.382484 | — | — |
| 60 | TC15001129.hg.1 | 1.8246391 | 4.616064 | 5.159258 | 0.0008785 | 0.0008785 | -3.382484 | — | — |
| 61 | TC15001157.hg.1 | 1.8246391 | 4.616064 | 5.159258 | 0.0008785 | 0.0008785 | -3.382484 | — | — |
| 62 | TC15001673.hg.1 | 1.8246391 | 4.616064 | 5.159258 | 0.0008785 | 0.0008785 | -3.382484 | — | — |
| 15 | TC0X001951.hg.1 | 1.8189778 | 4.444599 | 7.050275 | 0.0001098 | 0.0001098 | -3.175732 | — | — |
| 181 | 47420665_st | 1.8092450 | 2.108061 | 4.148134 | 0.0032534 | 0.0032534 | -3.567331 | — | — |
| 1 | TC6_dbb_hap3000083.hg.1 | 1.7364258 | 4.021221 | 11.872761 | 0.0000024 | 0.0000024 | -2.977216 | HLA-DRA | major histocompatibility complex, class II, DR alpha |
| 6 | TC6_mann_hap4000074.hg.1 | 1.6695281 | 4.118256 | 11.221229 | 0.0000037 | 0.0000037 | -2.991608 | HLA-DRA | major histocompatibility complex, class II, DR alpha |
| 3 | TC6_mcf_hap5000075.hg.1 | 1.6649864 | 4.117026 | 11.243423 | 0.0000037 | 0.0000037 | -2.991081 | HLA-DRA | major histocompatibility complex, class II, DR alpha |
| 4 | TC6_qbl_hap6000081.hg.1 | 1.6649864 | 4.117026 | 11.243423 | 0.0000037 | 0.0000037 | -2.991081 | HLA-DRA | major histocompatibility complex, class II, DR alpha |
| 5 | TC6_ssto_hap7000076.hg.1 | 1.6649864 | 4.117026 | 11.243423 | 0.0000037 | 0.0000037 | -2.991081 | HLA-DRA | major histocompatibility complex, class II, DR alpha |
| 2 | TC06000399.hg.1 | 1.6602617 | 3.999679 | 11.286359 | 0.0000036 | 0.0000036 | -2.990068 | HLA-DRA | major histocompatibility complex, class II, DR alpha |
| 124 | PSR06024774.hg.1 | -1.6480842 | 3.486136 | -4.508144 | 0.0020065 | 0.0020065 | -3.493414 | — | — |
| 7 | TC6_cox_hap2000090.hg.1 | 1.5800729 | 3.909857 | 9.980765 | 0.0000089 | 0.0000089 | -3.026245 | HLA-DRA | major histocompatibility complex, class II, DR alpha |
| 20 | 47424018_st | -1.5773243 | 2.689304 | -5.974953 | 0.0003393 | 0.0003393 | -3.276256 | — | — |
| 28 | TC18000797.hg.1 | 1.5432635 | 4.714361 | 5.606665 | 0.0005156 | 0.0005156 | -3.320351 | — | — |
| 11 | TC11003477.hg.1 | 1.5282861 | 3.516779 | 7.461492 | 0.0000738 | 0.0000738 | -3.145915 | SAA4 | serum amyloid A4, constitutive |
| 113 | TC16000269.hg.1 | -1.5074228 | 3.413260 | -4.559366 | 0.0018761 | 0.0018761 | -3.483679 | — | — |
| 131 | TC08001062.hg.1 | -1.4966222 | 5.932169 | -4.475130 | 0.0020957 | 0.0020957 | -3.499787 | STC1 | stanniocalcin 1 |
| 186 | 47421529_st | 1.4851581 | 2.093812 | 4.138777 | 0.0032954 | 0.0032954 | -3.569387 | — | — |
| 157 | TC22000577.hg.1 | -1.4718483 | 2.949695 | -4.262416 | 0.0027849 | 0.0027849 | -3.542788 | — | — |
| 9 | 47420725_st | 1.4615942 | 2.187253 | 8.014321 | 0.0000444 | 0.0000444 | -3.111522 | — | — |
| 122 | 47421241_st | 1.4341128 | 2.656520 | 4.517065 | 0.0019831 | 0.0019831 | -3.491705 | — | — |
| 36 | TC02001238.hg.1 | -1.4117604 | 4.390431 | -5.451950 | 0.0006181 | 0.0006181 | -3.340696 | MAP2 | microtubule-associated protein 2 |
| 12 | TC15001895.hg.1 | -1.3963063 | 1.433147 | -7.284620 | 0.0000874 | 0.0000874 | -3.158253 | — | — |
| 138 | 47419884_st | -1.3962335 | 1.860523 | -4.404372 | 0.0023019 | 0.0023019 | -3.513715 | — | — |
| 41 | 47423221_st | 1.3390742 | 1.839781 | 5.336293 | 0.0007092 | 0.0007092 | -3.356674 | — | — |
| 21 | TC11001704.hg.1 | 1.3183269 | 1.914391 | 5.935725 | 0.0003545 | 0.0003545 | -3.280681 | — | — |
| 68 | TC12002734.hg.1 | -1.3161750 | 10.329069 | -5.119041 | 0.0009229 | 0.0009229 | -3.388586 | SLC2A3 | solute carrier family 2 (facilitated glucose transporter), member 3 |
| 159 | TC6_cox_hap2000100.hg.1 | -1.3044060 | 2.665726 | -4.252875 | 0.0028211 | 0.0028211 | -3.544797 | HCG24 | HLA complex group 24 |
| 93 | TC20000876.hg.1 | -1.2955753 | 8.177874 | -4.740065 | 0.0014846 | 0.0014846 | -3.450785 | SLPI | secretory leukocyte peptidase inhibitor |
| 74 | 47424436_st | -1.2807591 | 1.851769 | -5.049985 | 0.0010048 | 0.0010048 | -3.399277 | — | — |
| 87 | 47424055_st | 1.2435919 | 1.433446 | 4.812428 | 0.0013536 | 0.0013536 | -3.438222 | — | — |
| 50 | TC19001622.hg.1 | -1.2429091 | 6.488263 | -5.177160 | 0.0008595 | 0.0008595 | -3.379797 | — | — |
| 227 | TC04000117.hg.1 | -1.2284320 | 3.123046 | -3.968485 | 0.0041705 | 0.0041705 | -3.608066 | — | — |
| 108 | TC02004032.hg.1 | 1.2272996 | 5.583444 | 4.608159 | 0.0017603 | 0.0017603 | -3.474577 | — | — |
| 172 | TC06000434.hg.1 | -1.2148922 | 3.119678 | -4.194146 | 0.0030553 | 0.0030553 | -3.557324 | — | — |
| 33 | TC12001907.hg.1 | -1.2111991 | 6.131961 | -5.486883 | 0.0005931 | 0.0005931 | -3.336002 | — | — |
| 35 | TC12001170.hg.1 | -1.2109123 | 9.257128 | -5.460716 | 0.0006117 | 0.0006117 | -3.339513 | SLC2A3 | solute carrier family 2 (facilitated glucose transporter), member 3 |
| 32 | 47424102_st | 1.2059030 | 1.736368 | 5.491920 | 0.0005896 | 0.0005896 | -3.335330 | — | — |
| 259 | TC02003749.hg.1 | -1.1880571 | 3.811939 | -3.884024 | 0.0046946 | 0.0046946 | -3.628163 | — | — |
| 207 | TC09001352.hg.1 | -1.1773506 | 1.635598 | -4.041638 | 0.0037672 | 0.0037672 | -3.591154 | — | — |
| 17 | TC15001710.hg.1 | 1.1647771 | 6.540506 | 6.333301 | 0.0002295 | 0.0002295 | -3.238546 | — | — |
| 230 | 3662480_st | 1.1537652 | 7.158878 | 3.964175 | 0.0041957 | 0.0041957 | -3.609077 | — | — |
| 120 | TC04001997.hg.1 | -1.1431700 | 2.702580 | -4.531446 | 0.0019460 | 0.0019460 | -3.488962 | — | — |
| 13 | TC05001205.hg.1 | 1.1349197 | 5.223500 | 7.204022 | 0.0000945 | 0.0000945 | -3.164114 | CDH10 | cadherin 10, type 2 (T2-cadherin) |
| 16 | TC02002499.hg.1 | -1.1160429 | 3.027889 | -6.561174 | 0.0001805 | 0.0001805 | -3.216901 | SCN9A | sodium channel, voltage-gated, type IX, alpha subunit |
| 18 | TC08001440.hg.1 | -1.0959806 | 4.787639 | -6.190944 | 0.0002676 | 0.0002676 | -3.252962 | TP53INP1 | tumor protein p53 inducible nuclear protein 1 |
| 26 | 47421979_st | -1.0945896 | 3.526882 | -5.679526 | 0.0004740 | 0.0004740 | -3.311158 | — | — |
| 14 | TC02002628.hg.1 | -1.0842553 | 3.832753 | -7.060002 | 0.0001088 | 0.0001088 | -3.174979 | TMEFF2 | transmembrane protein with EGF-like and two follistatin-like domains 2 |
| 75 | TC01003245.hg.1 | -1.0760953 | 5.883388 | -5.049497 | 0.0010054 | 0.0010054 | -3.399354 | FLG | filaggrin |
| 102 | 47419283_st | -1.0728938 | 1.969319 | -4.630072 | 0.0017109 | 0.0017109 | -3.470543 | — | — |
| 65 | TC01005829.hg.1 | -1.0676755 | 5.425159 | -5.133651 | 0.0009065 | 0.0009065 | -3.386358 | FLG | filaggrin |
| 103 | 3671548_st | 1.0649464 | 4.824891 | 4.629049 | 0.0017132 | 0.0017132 | -3.470731 | — | — |
| 268 | TC10002574.hg.1 | -1.0625140 | 4.520920 | -3.846481 | 0.0049499 | 0.0049499 | -3.637296 | LOC101929397 | uncharacterized LOC101929397 |
| 45 | TC18000331.hg.1 | 1.0513421 | 1.623643 | 5.295141 | 0.0007451 | 0.0007451 | -3.362524 | — | — |
| 126 | TC15000512.hg.1 | -1.0480840 | 3.722066 | -4.489440 | 0.0020565 | 0.0020565 | -3.497015 | — | — |
| 170 | TC08001816.hg.1 | -1.0431233 | 6.020214 | -4.199102 | 0.0030347 | 0.0030347 | -3.556257 | SLC7A2 | solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 |
| 40 | TC13000634.hg.1 | -1.0430193 | 5.447627 | -5.371703 | 0.0006798 | 0.0006798 | -3.351710 | SLC25A30 | solute carrier family 25, member 30 |
| 22 | TC06002112.hg.1 | -1.0286686 | 6.964645 | -5.889046 | 0.0003735 | 0.0003735 | -3.286027 | CTGF | connective tissue growth factor |
| 30 | TC0X000948.hg.1 | -1.0170142 | 5.112170 | -5.540506 | 0.0005570 | 0.0005570 | -3.328911 | TMEM47 | transmembrane protein 47 |
| 190 | 47419820_st | 1.0132997 | 1.448899 | 4.124418 | 0.0033609 | 0.0033609 | -3.572556 | — | — |
| 19 | TC02000927.hg.1 | -1.0099038 | 4.825662 | -6.057611 | 0.0003096 | 0.0003096 | -3.267131 | KIF5C | kinesin family member 5C |
| 112 | TC10000522.hg.1 | -1.0096445 | 4.322070 | -4.562917 | 0.0018674 | 0.0018674 | -3.483011 | — | — |
| 249 | TC16001352.hg.1 | 1.0048251 | 2.211975 | 3.902030 | 0.0045772 | 0.0045772 | -3.623827 | — | — |
| 188 | TC06000429.hg.1 | -0.9944716 | 4.178663 | -4.136041 | 0.0033078 | 0.0033078 | -3.569989 | — | — |
| 51 | 47419687_st | 0.9825656 | 1.488180 | 5.160640 | 0.0008770 | 0.0008770 | -3.382276 | — | — |
| 46 | TC19000805.hg.1 | -0.9812271 | 6.274601 | -5.270295 | 0.0007677 | 0.0007677 | -3.366100 | ERVV-2 | endogenous retrovirus group V, member 2 |
| 25 | TC01005828.hg.1 | -0.9809281 | 5.949490 | -5.754576 | 0.0004349 | 0.0004349 | -3.301938 | FLG | filaggrin |
| 175 | TC12002552.hg.1 | -0.9799902 | 5.767873 | -4.184455 | 0.0030959 | 0.0030959 | -3.559418 | — | — |
| 83 | TC15001949.hg.1 | 0.9796920 | 4.088601 | 4.898808 | 0.0012135 | 0.0012135 | -3.423661 | — | — |
| 252 | 47423307_st | -0.9767491 | 1.589235 | -3.898999 | 0.0045967 | 0.0045967 | -3.624555 | — | — |
| 109 | TC14001601.hg.1 | 0.9728365 | 3.884566 | 4.597682 | 0.0017845 | 0.0017845 | -3.476517 | — | — |
| 47 | TC15001907.hg.1 | -0.9649461 | 2.345389 | -5.240144 | 0.0007962 | 0.0007962 | -3.370483 | — | — |
| 82 | TC13000234.hg.1 | -0.9612145 | 3.523813 | -4.928283 | 0.0011694 | 0.0011694 | -3.418799 | PCDH17 | protocadherin 17 |
| 201 | 47419787_st | -0.9611395 | 1.549715 | -4.061800 | 0.0036636 | 0.0036636 | -3.586572 | — | — |
| 241 | 47422090_st | -0.9570081 | 2.270161 | -3.921016 | 0.0044568 | 0.0044568 | -3.619285 | — | — |
| 142 | TC08002373.hg.1 | 0.9540273 | 4.588725 | 4.371484 | 0.0024051 | 0.0024051 | -3.520315 | — | — |
| 176 | TC04002771.hg.1 | 0.9512695 | 5.089020 | 4.179653 | 0.0031162 | 0.0031162 | -3.560458 | ZNF827 | zinc finger protein 827 |
| 168 | TC05002612.hg.1 | -0.9497423 | 5.814343 | -4.205138 | 0.0030099 | 0.0030099 | -3.554959 | SLC12A2 | solute carrier family 12 (sodium/potassium/chloride transporter), member 2 |
| 236 | TC11002216.hg.1 | 0.9475860 | 2.058663 | 3.939046 | 0.0043457 | 0.0043457 | -3.615001 | — | — |
| 139 | TC06000010.hg.1 | 0.9465836 | 5.812012 | 4.401504 | 0.0023107 | 0.0023107 | -3.514287 | FOXF2 | forkhead box F2 |
| 70 | 47423846_st | -0.9461408 | 1.295035 | -5.116508 | 0.0009257 | 0.0009257 | -3.388973 | — | — |
| 88 | TC08001992.hg.1 | 0.9397066 | 2.394108 | 4.796574 | 0.0013812 | 0.0013812 | -3.440945 | — | — |
| 100 | TC14001401.hg.1 | -0.9378662 | 1.643793 | -4.659358 | 0.0016472 | 0.0016472 | -3.465203 | — | — |
| 155 | TC10001443.hg.1 | 0.9251172 | 3.773911 | 4.295429 | 0.0026635 | 0.0026635 | -3.535889 | — | — |
| 115 | TC01003878.hg.1 | 0.9204077 | 4.217955 | 4.543928 | 0.0019144 | 0.0019144 | -3.486593 | RNU6-1319P | RNA, U6 small nuclear 1319, pseudogene |
| 116 | TC01004037.hg.1 | 0.9204077 | 4.217955 | 4.543928 | 0.0019144 | 0.0019144 | -3.486593 | RNU6-747P | RNA, U6 small nuclear 747, pseudogene |
| 117 | TC07000284.hg.1 | 0.9204077 | 4.217955 | 4.543928 | 0.0019144 | 0.0019144 | -3.486593 | RNU6-241P | RNA, U6 small nuclear 241, pseudogene |
| 24 | TC06002990.hg.1 | 0.9072919 | 7.095794 | 5.758820 | 0.0004328 | 0.0004328 | -3.301424 | GTF3C6 | general transcription factor IIIC, polypeptide 6, alpha 35kDa |
| 253 | 3676043_st | 0.9067414 | 8.992440 | 3.896725 | 0.0046115 | 0.0046115 | -3.625101 | — | — |
| 178 | TC11001303.hg.1 | 0.9047489 | 2.343603 | 4.158016 | 0.0032097 | 0.0032097 | -3.565167 | RNU6-1143P | RNA, U6 small nuclear 1143, pseudogene |
| 98 | TC17001820.hg.1 | 0.9026516 | 5.551324 | 4.699852 | 0.0015633 | 0.0015633 | -3.457915 | SLC16A6 | solute carrier family 16, member 6 |
| 101 | PSR02023982.hg.1 | 0.8976339 | 4.041439 | 4.639484 | 0.0016902 | 0.0016902 | -3.468821 | — | — |
| 222 | TC03000768.hg.1 | -0.8971410 | 6.515891 | -3.983342 | 0.0040850 | 0.0040850 | -3.604595 | PLS1 | plastin 1 |
| 29 | TC15000913.hg.1 | -0.8923050 | 1.370365 | -5.559276 | 0.0005449 | 0.0005449 | -3.326462 | — | — |
| 23 | TC12000656.hg.1 | 0.8888859 | 4.274430 | 5.813832 | 0.0004066 | 0.0004066 | -3.294832 | NAV3 | neuron navigator 3 |
| 78 | 2909164_st | -0.8784470 | 6.678777 | -5.023932 | 0.0010378 | 0.0010378 | -3.403382 | — | — |
| 147 | TC12001168.hg.1 | -0.8777512 | 6.354506 | -4.352140 | 0.0024681 | 0.0024681 | -3.524234 | SLC2A14 | solute carrier family 2 (facilitated glucose transporter), member 14 |
| 42 | TC05002783.hg.1 | 0.8744668 | 5.483123 | 5.332880 | 0.0007121 | 0.0007121 | -3.357156 | — | — |
| 72 | TC19000303.hg.1 | 0.8677113 | 4.175099 | 5.085603 | 0.0009616 | 0.0009616 | -3.393728 | — | — |
| 145 | TC04001283.hg.1 | 0.8650210 | 3.787979 | 4.359749 | 0.0024431 | 0.0024431 | -3.522689 | CXCL5 | chemokine (C-X-C motif) ligand 5 |
| 85 | TC01001306.hg.1 | -0.8629704 | 3.121130 | -4.874537 | 0.0012512 | 0.0012512 | -3.427705 | SYT11 | synaptotagmin XI |
| 121 | TC03000482.hg.1 | -0.8554361 | 2.572256 | -4.524378 | 0.0019641 | 0.0019641 | -3.490308 | OR5AC2 | olfactory receptor, family 5, subfamily AC, member 2 |
| 81 | TC03001057.hg.1 | 0.8552271 | 2.999343 | 4.940008 | 0.0011523 | 0.0011523 | -3.416879 | RP11-655G22.1 | novel trancript |
| 114 | TC03000892.hg.1 | -0.8538817 | 5.787769 | -4.555179 | 0.0018864 | 0.0018864 | -3.484468 | SERPINI1 | serpin peptidase inhibitor, clade I (neuroserpin), member 1 |
| 141 | 47422093_st | -0.8493589 | 2.380390 | -4.382030 | 0.0023715 | 0.0023715 | -3.518189 | — | — |
| 214 | 47420513_st | -0.8474702 | 1.786096 | -4.021389 | 0.0038745 | 0.0038745 | -3.595790 | — | — |
| 31 | TC03002727.hg.1 | 0.8472723 | 2.250786 | 5.509799 | 0.0005774 | 0.0005774 | -3.332955 | — | — |
| 77 | TC15000968.hg.1 | 0.8454604 | 3.670053 | 5.032467 | 0.0010269 | 0.0010269 | -3.402033 | — | — |
| 34 | TC03000275.hg.1 | -0.8445567 | 2.015274 | -5.479850 | 0.0005981 | 0.0005981 | -3.336942 | MIR4443 | microRNA 4443 |
| 220 | 47424238_st | 0.8435727 | 1.544014 | 3.988953 | 0.0040532 | 0.0040532 | -3.603289 | — | — |
| 63 | TC6_mcf_hap5000213.hg.1 | 0.8408503 | 6.147923 | 5.134538 | 0.0009055 | 0.0009055 | -3.386223 | CFB | complement factor B |
| 64 | TC6_ssto_hap7000199.hg.1 | 0.8408503 | 6.147923 | 5.134538 | 0.0009055 | 0.0009055 | -3.386223 | CFB | complement factor B |
| 49 | TC07002501.hg.1 | 0.8402226 | 6.241683 | 5.211356 | 0.0008245 | 0.0008245 | -3.374713 | CUX1 | cut-like homeobox 1 |
| 265 | 2960249_st | 0.8375813 | 4.028793 | 3.866076 | 0.0048148 | 0.0048148 | -3.632514 | — | — |
| 173 | TC10000401.hg.1 | 0.8372576 | 5.993515 | 4.193597 | 0.0030575 | 0.0030575 | -3.557443 | MYPN | myopalladin |
| 71 | TC6_dbb_hap3000222.hg.1 | 0.8369553 | 6.149681 | 5.099484 | 0.0009453 | 0.0009453 | -3.391586 | CFB | complement factor B |
| 211 | TC14001140.hg.1 | -0.8369361 | 5.741637 | -4.031315 | 0.0038215 | 0.0038215 | -3.593513 | TXNDC16 | thioredoxin domain containing 16 |
| 73 | TC6_qbl_hap6000225.hg.1 | 0.8339594 | 6.150726 | 5.068983 | 0.0009815 | 0.0009815 | -3.396308 | CFB | complement factor B |
| 223 | TC0X002342.hg.1 | -0.8298784 | 3.212648 | -3.982243 | 0.0040912 | 0.0040912 | -3.604851 | SPANXC | SPANX family, member C |
| 134 | TC09001890.hg.1 | 0.8286581 | 4.412597 | 4.440846 | 0.0021930 | 0.0021930 | -3.506490 | RPL36AP33 | ribosomal protein L36a pseudogene 33 |
| 44 | TC0X000188.hg.1 | 0.8283608 | 6.098042 | 5.314085 | 0.0007283 | 0.0007283 | -3.359820 | — | — |
| 76 | TC6_cox_hap2000245.hg.1 | 0.8270667 | 6.150349 | 5.037820 | 0.0010201 | 0.0010201 | -3.401189 | CFB | complement factor B |
| 105 | TC11001685.hg.1 | 0.8264321 | 4.293853 | 4.619888 | 0.0017337 | 0.0017337 | -3.472414 | — | — |
| 164 | TC01002849.hg.1 | 0.8233586 | 5.248295 | 4.230351 | 0.0029085 | 0.0029085 | -3.549570 | GBP4 | guanylate binding protein 4 |
| 263 | 47419399_st | 0.8209049 | 1.376656 | 3.867263 | 0.0048068 | 0.0048068 | -3.632225 | — | — |
| 167 | TC03002444.hg.1 | 0.8207990 | 2.599446 | 4.207501 | 0.0030002 | 0.0030002 | -3.554452 | — | — |
| 67 | TC06004077.hg.1 | 0.8182740 | 6.075330 | 5.120884 | 0.0009208 | 0.0009208 | -3.388304 | CFB | complement factor B |
| 95 | TC14000794.hg.1 | 0.8181480 | 7.508470 | 4.713652 | 0.0015358 | 0.0015358 | -3.455456 | TNFAIP2 | tumor necrosis factor, alpha-induced protein 2 |
| 80 | 47421299_st | -0.8124930 | 1.662695 | -4.943964 | 0.0011466 | 0.0011466 | -3.416234 | — | — |
| 111 | 3615298_st | 0.8118762 | 8.205502 | 4.572996 | 0.0018429 | 0.0018429 | -3.481120 | — | — |
| 150 | TC15002295.hg.1 | 0.8077203 | 3.828816 | 4.314295 | 0.0025967 | 0.0025967 | -3.531985 | — | — |
| 189 | TC0X000727.hg.1 | -0.8074459 | 4.709963 | -4.135503 | 0.0033102 | 0.0033102 | -3.570108 | HMGB3 | high mobility group box 3 |
| 177 | TC11001672.hg.1 | 0.8063181 | 1.748819 | 4.175541 | 0.0031338 | 0.0031338 | -3.561350 | — | — |
| 250 | TC18000564.hg.1 | -0.8056253 | 5.081183 | -3.900553 | 0.0045867 | 0.0045867 | -3.624181 | DSEL | dermatan sulfate epimerase-like |
| 144 | TC06003522.hg.1 | -0.8051482 | 3.074953 | -4.361646 | 0.0024369 | 0.0024369 | -3.522304 | — | — |
| 43 | TC12002930.hg.1 | 0.8047076 | 4.019578 | 5.332844 | 0.0007121 | 0.0007121 | -3.357161 | — | — |
| 104 | TC10000258.hg.1 | 0.8031137 | 4.364083 | 4.624431 | 0.0017235 | 0.0017235 | -3.471579 | RNU6-1118P | RNA, U6 small nuclear 1118, pseudogene |
| 127 | TC21000560.hg.1 | 0.8009137 | 6.496864 | 4.489191 | 0.0020572 | 0.0020572 | -3.497063 | — | — |
| 107 | TC12002835.hg.1 | -0.7997320 | 4.241214 | -4.611179 | 0.0017534 | 0.0017534 | -3.474019 | — | — |
| 243 | TC08000324.hg.1 | -0.7978501 | 6.594341 | -3.918700 | 0.0044713 | 0.0044713 | -3.619837 | AP3M2 | adaptor-related protein complex 3, mu 2 subunit |
| 106 | TC08000694.hg.1 | -0.7951082 | 3.938238 | -4.618289 | 0.0017373 | 0.0017373 | -3.472708 | COLEC10 | collectin sub-family member 10 (C-type lectin) |
| 200 | TC19001418.hg.1 | 0.7937023 | 1.892858 | 4.069221 | 0.0036263 | 0.0036263 | -3.584894 | — | — |
| 84 | TC0X000847.hg.1 | 0.7895641 | 4.458944 | 4.898520 | 0.0012139 | 0.0012139 | -3.423709 | — | — |
| 125 | TC19000081.hg.1 | -0.7858046 | 4.768912 | -4.499106 | 0.0020305 | 0.0020305 | -3.495151 | CREB3L3 | cAMP responsive element binding protein 3-like 3 |
| 183 | TC12001282.hg.1 | -0.7853104 | 5.788827 | -4.142051 | 0.0032806 | 0.0032806 | -3.568667 | EPS8 | epidermal growth factor receptor pathway substrate 8 |
| 160 | TC10002067.hg.1 | 0.7818377 | 2.102672 | 4.250768 | 0.0028291 | 0.0028291 | -3.545242 | — | — |
| 246 | 47419854_st | 0.7808379 | 1.124662 | 3.906729 | 0.0045471 | 0.0045471 | -3.622700 | — | — |
| 128 | TC08000482.hg.1 | -0.7805112 | 6.875943 | -4.487473 | 0.0020619 | 0.0020619 | -3.497395 | RDH10 | retinol dehydrogenase 10 (all-trans) |
| 94 | TC10001334.hg.1 | -0.7801463 | 7.703571 | -4.738897 | 0.0014868 | 0.0014868 | -3.450991 | — | — |
| 240 | TC15001429.hg.1 | 0.7745617 | 3.473497 | 3.925781 | 0.0044272 | 0.0044272 | -3.618150 | — | — |
| 146 | TC08001736.hg.1 | -0.7726730 | 4.199063 | -4.353095 | 0.0024650 | 0.0024650 | -3.524040 | EPPK1 | epiplakin 1 |
| 96 | TC09002683.hg.1 | -0.7716138 | 2.081326 | -4.711238 | 0.0015406 | 0.0015406 | -3.455885 | RP11-23B15.1 | putative novel transcript |
| 169 | 47422398_st | -0.7705368 | 2.241157 | -4.200823 | 0.0030276 | 0.0030276 | -3.555886 | — | — |
| 90 | TC03003286.hg.1 | 0.7691092 | 3.558113 | 4.755597 | 0.0014554 | 0.0014554 | -3.448060 | — | — |
| 196 | TC11001227.hg.1 | 0.7664856 | 4.331568 | 4.092022 | 0.0035140 | 0.0035140 | -3.579766 | RNU6-447P | RNA, U6 small nuclear 447, pseudogene |
| 137 | TC07002670.hg.1 | 0.7648118 | 5.753313 | 4.417598 | 0.0022618 | 0.0022618 | -3.511084 | — | — |
| 99 | TC22001203.hg.1 | 0.7646673 | 4.799403 | 4.678519 | 0.0016069 | 0.0016069 | -3.461741 | XXbac-B33L19.6 | putative novel transcript |
| 245 | TC05000070.hg.1 | -0.7623634 | 2.969341 | -3.913730 | 0.0045026 | 0.0045026 | -3.621024 | CTD-2199O4.1 | novel transcript |
| 37 | TC19002526.hg.1 | -0.7595084 | 5.273655 | -5.451290 | 0.0006185 | 0.0006185 | -3.340786 | — | — |
| 185 | TC13001561.hg.1 | -0.7573711 | 1.964871 | -4.139264 | 0.0032932 | 0.0032932 | -3.569280 | — | — |
| 163 | TC03002386.hg.1 | 0.7555364 | 2.306833 | 4.231385 | 0.0029044 | 0.0029044 | -3.549350 | — | — |
| 92 | TC18000524.hg.1 | 0.7550038 | 2.827281 | 4.746484 | 0.0014724 | 0.0014724 | -3.449657 | CCDC68 | coiled-coil domain containing 68 |
| 79 | 3676041_st | 0.7526350 | 9.118872 | 4.988422 | 0.0010847 | 0.0010847 | -3.409042 | — | — |
| 254 | 3080337_st | 0.7497764 | 6.783507 | 3.896104 | 0.0046155 | 0.0046155 | -3.625251 | — | — |
| 154 | TC08001253.hg.1 | -0.7487841 | 4.520402 | -4.298766 | 0.0026516 | 0.0026516 | -3.535196 | CA8 | carbonic anhydrase VIII |
| 129 | TC07000874.hg.1 | 0.7482208 | 2.165423 | 4.479950 | 0.0020824 | 0.0020824 | -3.498852 | PP12708 | — |
| 180 | TC15000904.hg.1 | -0.7464206 | 5.980295 | -4.151478 | 0.0032386 | 0.0032386 | -3.566598 | — | — |
| 260 | TC09000364.hg.1 | -0.7412710 | 3.992747 | -3.881222 | 0.0047132 | 0.0047132 | -3.628840 | — | — |
| 204 | PSR07002495.hg.1 | 0.7339653 | 6.810561 | 4.049060 | 0.0037287 | 0.0037287 | -3.589463 | — | — |
| 66 | TC6_mann_hap4000196.hg.1 | 0.7337230 | 6.184528 | 5.121146 | 0.0009205 | 0.0009205 | -3.388264 | CFB | complement factor B |
| 244 | TC11001374.hg.1 | 0.7335355 | 2.788817 | 3.917828 | 0.0044768 | 0.0044768 | -3.620045 | — | — |
| 264 | TC18000078.hg.1 | 0.7309407 | 3.543635 | 3.866516 | 0.0048118 | 0.0048118 | -3.632407 | RNU6-316P | RNA, U6 small nuclear 316, pseudogene |
| 231 | PSR17008081.hg.1 | 0.7299395 | 6.158249 | 3.962078 | 0.0042080 | 0.0042080 | -3.609569 | — | — |
| 97 | TC0X001317.hg.1 | -0.7286902 | 1.930718 | -4.707854 | 0.0015473 | 0.0015473 | -3.456487 | RP3-327A19.5 | novel transcript, antisense to AKAP14 |
| 174 | TC04001615.hg.1 | 0.7280193 | 6.007871 | 4.190982 | 0.0030685 | 0.0030685 | -3.558007 | ZNF827 | zinc finger protein 827 |
| 123 | TC21000036.hg.1 | -0.7259438 | 2.441798 | -4.512972 | 0.0019938 | 0.0019938 | -3.492488 | RNU6-1326P | RNA, U6 small nuclear 1326, pseudogene |
| 149 | TC0X002341.hg.1 | -0.7212637 | 4.009933 | -4.334538 | 0.0025271 | 0.0025271 | -3.527825 | SPANXA1 | sperm protein associated with the nucleus, X-linked, family member A1 |
| 69 | TC05002634.hg.1 | 0.7197046 | 6.672090 | 5.117982 | 0.0009241 | 0.0009241 | -3.388747 | JADE2 | jade family PHD finger 2 |
| 133 | TC06000242.hg.1 | 0.7184419 | 2.432489 | 4.449236 | 0.0021688 | 0.0021688 | -3.504842 | — | — |
| 195 | TC0X001792.hg.1 | 0.7107672 | 3.033972 | 4.092779 | 0.0035104 | 0.0035104 | -3.579597 | SYTL4 | synaptotagmin-like 4 |
| 110 | TC19000293.hg.1 | -0.7105321 | 7.072137 | -4.580395 | 0.0018252 | 0.0018252 | -3.479736 | — | — |
| 255 | TC07000774.hg.1 | 0.7064419 | 6.007585 | 3.895015 | 0.0046226 | 0.0046226 | -3.625513 | — | — |
| 256 | TC08001586.hg.1 | 0.7064419 | 6.007585 | 3.895015 | 0.0046226 | 0.0046226 | -3.625513 | — | — |
| 130 | TC02004646.hg.1 | 0.7062535 | 3.150427 | 4.479826 | 0.0020828 | 0.0020828 | -3.498876 | — | — |
| 135 | TC10002313.hg.1 | 0.7053321 | 3.479205 | 4.436471 | 0.0022058 | 0.0022058 | -3.507351 | RP11-328K15.1 | putative novel transcript |
| 248 | TC15001153.hg.1 | 0.7011411 | 7.337381 | 3.902538 | 0.0045739 | 0.0045739 | -3.623705 | — | — |
| 208 | TC19000439.hg.1 | 0.6989013 | 6.944991 | 4.040804 | 0.0037716 | 0.0037716 | -3.591344 | KCTD15 | potassium channel tetramerization domain containing 15 |
| 153 | TC02002817.hg.1 | -0.6968342 | 1.920422 | -4.306451 | 0.0026243 | 0.0026243 | -3.533605 | — | — |
| 262 | TC02002436.hg.1 | 0.6963666 | 4.458407 | 3.872414 | 0.0047720 | 0.0047720 | -3.630974 | AC012501.2 | putative novel transcript |
| 209 | TC18000909.hg.1 | 0.6940239 | 3.191854 | 4.036624 | 0.0037935 | 0.0037935 | -3.592299 | — | — |
| 136 | TC05002022.hg.1 | -0.6911415 | 1.704451 | -4.427738 | 0.0022315 | 0.0022315 | -3.509075 | RNU6-168P | RNA, U6 small nuclear 168, pseudogene |
| 91 | TC10000544.hg.1 | -0.6883851 | 2.405286 | -4.748258 | 0.0014691 | 0.0014691 | -3.449346 | — | — |
| 148 | TC12002570.hg.1 | 0.6855918 | 4.373392 | 4.350743 | 0.0024728 | 0.0024728 | -3.524518 | ADAM1A | ADAM metallopeptidase domain 1A, pseudogene |
| 158 | TC0X002210.hg.1 | -0.6828448 | 2.116250 | -4.259829 | 0.0027946 | 0.0027946 | -3.543332 | — | — |
| 229 | TC01004099.hg.1 | 0.6822668 | 3.386587 | 3.965504 | 0.0041879 | 0.0041879 | -3.608765 | RP11-34P13.9 | putative novel transcript |
| 232 | TC10002623.hg.1 | 0.6815146 | 5.603294 | 3.960423 | 0.0042177 | 0.0042177 | -3.609958 | — | — |
| 202 | TC20000684.hg.1 | 0.6800001 | 4.208193 | 4.060574 | 0.0036698 | 0.0036698 | -3.586849 | RP5-1096J16.1 | novel transcript |
| 151 | TC11001505.hg.1 | 0.6794497 | 2.771855 | 4.312484 | 0.0026030 | 0.0026030 | -3.532358 | MUC15 | mucin 15, cell surface associated |
| 218 | TC09001479.hg.1 | -0.6777520 | 4.651295 | -4.003312 | 0.0039730 | 0.0039730 | -3.599958 | RNY4P18 | RNA, Ro-associated Y4 pseudogene 18 |
| 118 | TC08002024.hg.1 | 0.6765574 | 2.826270 | 4.542616 | 0.0019177 | 0.0019177 | -3.486842 | — | — |
| 247 | 3475642_st | -0.6754552 | 10.375751 | -3.903270 | 0.0045692 | 0.0045692 | -3.623529 | — | — |
| 89 | TC06001952.hg.1 | -0.6747011 | 2.545895 | -4.766417 | 0.0014354 | 0.0014354 | -3.446171 | EPHA7 | EPH receptor A7 |
| 132 | TC02000237.hg.1 | 0.6654975 | 5.218370 | 4.466906 | 0.0021186 | 0.0021186 | -3.501387 | QPCT | glutaminyl-peptide cyclotransferase |
| 191 | 3371074_st | 0.6591336 | 7.627872 | 4.115090 | 0.0034043 | 0.0034043 | -3.574623 | — | — |
| 199 | TC14001955.hg.1 | 0.6553476 | 4.031909 | 4.076040 | 0.0035923 | 0.0035923 | -3.583356 | — | — |
| 171 | TC03000021.hg.1 | 0.6525359 | 5.260091 | 4.196575 | 0.0030452 | 0.0030452 | -3.556801 | AC069277.2 | novel transcript |
| 161 | TC04000122.hg.1 | 0.6489222 | 2.265269 | 4.246523 | 0.0028454 | 0.0028454 | -3.546139 | — | — |
| 166 | TC17001951.hg.1 | -0.6486904 | 3.544385 | -4.208426 | 0.0029964 | 0.0029964 | -3.554253 | MIR3186 | microRNA 3186 |
| 210 | TC02002827.hg.1 | 0.6455148 | 5.917383 | 4.035407 | 0.0037999 | 0.0037999 | -3.592577 | DOCK10 | dedicator of cytokinesis 10 |
| 233 | TC09002054.hg.1 | -0.6451089 | 1.660053 | -3.958926 | 0.0042265 | 0.0042265 | -3.610310 | — | — |
| 212 | TC09002641.hg.1 | 0.6434764 | 2.643924 | 4.025197 | 0.0038541 | 0.0038541 | -3.594915 | — | — |
| 239 | TC03000405.hg.1 | -0.6431977 | 3.058818 | -3.936770 | 0.0043595 | 0.0043595 | -3.615540 | MAGI1-AS1 | MAGI1 antisense RNA 1 |
| 182 | TC01000477.hg.1 | -0.6418522 | 3.004895 | -4.147173 | 0.0032577 | 0.0032577 | -3.567542 | — | — |
| 235 | TC05002340.hg.1 | -0.6409260 | 2.113583 | -3.943810 | 0.0043168 | 0.0043168 | -3.613874 | — | — |
| 184 | TC11001674.hg.1 | -0.6408844 | 2.286587 | -4.140237 | 0.0032888 | 0.0032888 | -3.569066 | — | — |
| 119 | TC18000208.hg.1 | 0.6374043 | 6.400822 | 4.542128 | 0.0019189 | 0.0019189 | -3.486934 | ZNF532 | zinc finger protein 532 |
| 206 | TC15002232.hg.1 | -0.6357077 | 4.218051 | -4.044081 | 0.0037545 | 0.0037545 | -3.590597 | TLN2 | talin 2 |
| 251 | 3662477_st | 0.6350424 | 6.701402 | 3.900144 | 0.0045893 | 0.0045893 | -3.624280 | — | — |
| 165 | TC19001563.hg.1 | -0.6341093 | 6.097101 | -4.210165 | 0.0029894 | 0.0029894 | -3.553880 | ATP1A3 | ATPase, Na+/K+ transporting, alpha 3 polypeptide |
| 143 | TC05000494.hg.1 | 0.6240093 | 2.117060 | 4.371189 | 0.0024061 | 0.0024061 | -3.520374 | RP11-58B2.1 | novel transcript |
| 228 | TC07003221.hg.1 | 0.6235236 | 2.428482 | 3.968432 | 0.0041708 | 0.0041708 | -3.608079 | AC006007.1 | novel transcript |
| 140 | TC19001925.hg.1 | 0.6193665 | 4.586438 | 4.397079 | 0.0023244 | 0.0023244 | -3.515172 | — | — |
| 162 | 3151626_st | 0.6187273 | 8.261256 | 4.237552 | 0.0028802 | 0.0028802 | -3.548039 | — | — |
| 203 | TC16001503.hg.1 | 0.6187223 | 4.028525 | 4.051704 | 0.0037151 | 0.0037151 | -3.588862 | — | — |
| 242 | TC12003243.hg.1 | -0.6157111 | 5.963796 | -3.920761 | 0.0044584 | 0.0044584 | -3.619346 | ERBB3 | v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3 |
| 187 | TC08001683.hg.1 | 0.6154342 | 6.766000 | 4.137079 | 0.0033031 | 0.0033031 | -3.569761 | CASC7 | cancer susceptibility candidate 7 (non-protein coding) |
| 258 | TC01005732.hg.1 | 0.6104743 | 6.220089 | 3.885342 | 0.0046859 | 0.0046859 | -3.627845 | CD58 | CD58 molecule |
| 217 | TC11002583.hg.1 | 0.6101696 | 4.229620 | 4.008142 | 0.0039464 | 0.0039464 | -3.598842 | KCNC1 | potassium voltage-gated channel, Shaw-related subfamily, member 1 |
| 179 | TC20001333.hg.1 | 0.6053640 | 6.140878 | 4.153654 | 0.0032289 | 0.0032289 | -3.566122 | — | — |
| 198 | TC10001196.hg.1 | -0.6040145 | 4.586791 | -4.076294 | 0.0035910 | 0.0035910 | -3.583299 | LOC101929397 | uncharacterized LOC101929397 |
| 221 | TC12000800.hg.1 | -0.6015607 | 1.546013 | -3.983611 | 0.0040835 | 0.0040835 | -3.604532 | — | — |
| 238 | PSR17016921.hg.1 | 0.5988230 | 8.418035 | 3.937346 | 0.0043560 | 0.0043560 | -3.615404 | — | — |
| 215 | TC01002750.hg.1 | -0.5955574 | 2.515284 | -4.010763 | 0.0039321 | 0.0039321 | -3.598237 | RNU4-88P | RNA, U4 small nuclear 88, pseudogene |
| 257 | TC06001954.hg.1 | -0.5937483 | 2.236153 | -3.891701 | 0.0046442 | 0.0046442 | -3.626311 | RNU4-70P | RNA, U4 small nuclear 70, pseudogene |
| 156 | TC11000630.hg.1 | -0.5931577 | 6.050826 | -4.265225 | 0.0027743 | 0.0027743 | -3.542197 | LOC101927789 | putative ubiquitin-like protein FUBI-like protein ENSP00000310146-like |
| 194 | TC07002857.hg.1 | -0.5906470 | 1.555560 | -4.101662 | 0.0034677 | 0.0034677 | -3.577612 | HOXA13 | homeobox A13 |
| 237 | TC06000886.hg.1 | 0.5899474 | 6.465504 | 3.938735 | 0.0043476 | 0.0043476 | -3.615075 | GTF3C6 | general transcription factor IIIC, polypeptide 6, alpha 35kDa |
| 224 | 3670189_st | 0.5886504 | 9.682810 | 3.980332 | 0.0041022 | 0.0041022 | -3.605296 | — | — |
| 234 | TC01005886.hg.1 | -0.5872906 | 4.309395 | -3.953853 | 0.0042566 | 0.0042566 | -3.611503 | — | — |
| 225 | TC03003236.hg.1 | 0.5854098 | 2.295588 | 3.974163 | 0.0041376 | 0.0041376 | -3.606737 | — | — |
| 205 | TC07002886.hg.1 | 0.5824221 | 3.234605 | 4.045266 | 0.0037484 | 0.0037484 | -3.590327 | TBX20 | T-box 20 |
| 266 | TC09000899.hg.1 | -0.5741384 | 5.532533 | -3.849624 | 0.0049279 | 0.0049279 | -3.636527 | GLDC | glycine dehydrogenase (decarboxylating) |
| 197 | TC04000102.hg.1 | 0.5686482 | 4.446222 | 4.083656 | 0.0035548 | 0.0035548 | -3.581643 | USP17L23 | ubiquitin specific peptidase 17-like family member 23 |
| 226 | TC08000695.hg.1 | -0.5538399 | 8.788362 | -3.968536 | 0.0041702 | 0.0041702 | -3.608054 | MAL2 | mal, T-cell differentiation protein 2 (gene/pseudogene) |
| 261 | TC22001312.hg.1 | -0.5517385 | 2.145890 | -3.879991 | 0.0047213 | 0.0047213 | -3.629138 | — | — |
| 267 | TC15001997.hg.1 | -0.5373415 | 2.426173 | -3.846983 | 0.0049464 | 0.0049464 | -3.637173 | RNU6-322P | RNA, U6 small nuclear 322, pseudogene |
Note that this table has been sorted from largest to smallest absolute log-fold-change (logFC). One point of contention here is that many of these logFC are quite small… however, a logFC of 0.5 still means a 40% alteration in expression; not something to regard as irrelevant perhaps?
over.rep <- read.csv("DE_filtering_testing/nonadjusted.pvalue.overrep.tab", sep="\t")
over.rep.simple <- over.rep[c(3,4,5,1,2,6)]
kable(over.rep.simple) %>%
kable_styling() %>%
scroll_box(width = "100%", height = "400px")| pathway | source | external_id | p.value | q.value | members_input_overlap |
|---|---|---|---|---|---|
| Rheumatoid arthritis - Homo sapiens (human) | KEGG | path:hsa05323 | 0.0004020 | 0.0321635 | CCL20; HLA-DRA; CXCL5; CXCL8 |
| Chemokine receptors bind chemokines | Reactome | R-HSA-380108 | 0.0009806 | 0.0392231 | CCL20; CXCL5; CXCL8 |
| Cellular hexose transport | Reactome | R-HSA-189200 | 0.0030245 | 0.0483405 | SLC2A14; SLC2A3 |
| Fructose and mannose metabolism | EHMN | Fructose and mannose metabolism | 0.0030245 | 0.0483405 | SLC2A14; SLC2A3 |
| PI3K-AKT-mTOR - VitD3 Signalling | Wikipathways | WP4141 | 0.0033186 | 0.0483405 | HLA-DRA; SLC2A3 |
| EBV LMP1 signaling | Wikipathways | WP262 | 0.0036255 | 0.0483405 | CXCL8; CCL20 |
| IL-17 signaling pathway - Homo sapiens (human) | KEGG | path:hsa04657 | 0.0057679 | 0.0659188 | CCL20; CXCL5; CXCL8 |
| TNF signaling pathway - Homo sapiens (human) | KEGG | path:hsa04668 | 0.0091564 | 0.0862528 | CREB3L3; CXCL5; CCL20 |
| Interleukin-10 signaling | Wikipathways | WP4063 | 0.0097034 | 0.0862528 | CXCL8; CCL20 |
| Galactose metabolism | EHMN | Galactose metabolism | 0.0128637 | 0.1014103 | SLC2A14; SLC2A3 |
| Heart Development | Wikipathways | WP1591 | 0.0145901 | 0.1014103 | TBX20; ERBB3 |
| SLC-mediated transmembrane transport | Reactome | R-HSA-425407 | 0.0152115 | 0.1014103 | SLC7A2; SLC2A14; SLC2A3; SLC12A2 |
| Staphylococcus aureus infection - Homo sapiens (human) | KEGG | path:hsa05150 | 0.0196482 | 0.1134639 | HLA-DRA; CFB |
| miR-targeted genes in muscle cell - TarBase | Wikipathways | WP2005 | 0.0198562 | 0.1134639 | ERBB3; TP53INP1; SLC12A2; RDH10; TNFAIP2 |
| Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways | Wikipathways | WP706 | 0.0244017 | 0.1301426 | MAP2; CXCL8; ATP1A3 |
| Lung fibrosis | Wikipathways | WP3624 | 0.0260853 | 0.1304263 | CXCL8; CTGF |
| Glucocorticoid Receptor Pathway | Wikipathways | WP2880 | 0.0316016 | 0.1363149 | CCL20; NAV3 |
| Thyroid hormone synthesis - Homo sapiens (human) | KEGG | path:hsa04918 | 0.0340948 | 0.1363149 | CREB3L3; ATP1A3 |
| Nuclear Receptors Meta-Pathway | Wikipathways | WP2882 | 0.0350739 | 0.1363149 | CCL20; NAV3; SLC2A14; SLC2A3 |
| Pertussis - Homo sapiens (human) | KEGG | path:hsa05133 | 0.0357984 | 0.1363149 | CXCL8; CXCL5 |
| Glycine, serine, alanine and threonine metabolism | EHMN | Glycine, serine, alanine and threonine metabolism | 0.0375345 | 0.1363149 | GLDC; SLC7A2 |
| Chemokine signaling pathway - Homo sapiens (human) | KEGG | path:hsa04062 | 0.0378985 | 0.1363149 | CCL20; CXCL5; CXCL8 |
| Peptide ligand-binding receptors | Reactome | R-HSA-375276 | 0.0404532 | 0.1363149 | CXCL8; CXCL5; CCL20 |
| miR-targeted genes in epithelium - TarBase | Wikipathways | WP2002 | 0.0412620 | 0.1363149 | TP53INP1; SLC12A2; RDH10; TNFAIP2 |
| Insulin secretion - Homo sapiens (human) | KEGG | path:hsa04911 | 0.0438582 | 0.1363149 | CREB3L3; ATP1A3 |
| Transport of small molecules | Reactome | R-HSA-382551 | 0.0445502 | 0.1363149 | SLC7A2; SLC2A14; SLC2A3; CREB3L3; ATP1A3; SLC12A2 |
| Salivary secretion - Homo sapiens (human) | KEGG | path:hsa04970 | 0.0486007 | 0.1363149 | ATP1A3; SLC12A2 |
| Allograft Rejection | Wikipathways | WP2328 | 0.0495708 | 0.1363149 | CXCL8; HLA-DRA |
This gives us a total of 28 over-representated pathways. Note that this can be further filtered by applying lower p-values.
Here, we ignore p-values and simmply focus on logFC being higher than 1 or less than -1.
eset <- project.bgcorrect.norm.avg.filt
fit <- lmFit(eset, design2)
fit <- eBayes(fit, trend=T, robust=T)
fit2 <- contrasts.fit(fit, c(0,0,0,-1,1))
fit2 <- eBayes(fit2)
diff.tGFR <- topTable(fit2, lfc = 1, number=Inf)
diff.tGFR <- setDT(diff.tGFR, keep.rownames = TRUE)[]
colnames(diff.tGFR)[1] <- "probe"
diff.tGFR <- dplyr::left_join(diff.tGFR,probe.gene.map,by="probe")
diff.tGFR.size <- diff.tGFR[order(-abs(diff.tGFR$logFC)),]
write.csv(diff.tGFR, "DE_filtering_testing/logFC.filtering.csv")
kable(diff.tGFR.size) %>%
kable_styling() %>%
scroll_box(width = "100%", height = "400px")| probe | logFC | AveExpr | t | P.Value | adj.P.Val | B | name | description | |
|---|---|---|---|---|---|---|---|---|---|
| 10 | 3597981_st | -3.656042 | 1.951490 | -7.830909 | 0.0000524 | 0.3693411 | -3.122281 | — | — |
| 177 | AFFX-r2-Bs-phe-5_st | -3.339590 | 6.315364 | -2.609773 | 0.0312757 | 0.9998332 | -4.012741 | — | — |
| 190 | AFFX-r2-Bs-thr-5_st | -3.301030 | 7.392850 | -2.484720 | 0.0379780 | 0.9998332 | -4.058769 | — | — |
| 121 | TC04002067.hg.1 | 2.994927 | 2.302627 | 3.245634 | 0.0118599 | 0.9998332 | -3.801190 | CXCL8 | chemokine (C-X-C motif) ligand 8 |
| 201 | AFFX-r2-Bs-dap-5_st | -2.989410 | 8.679186 | -2.354797 | 0.0464903 | 0.9998332 | -4.107929 | — | — |
| 199 | ERCC-00099_st | -2.971454 | 6.870018 | -2.385534 | 0.0443172 | 0.9998332 | -4.096183 | — | — |
| 145 | ERCCmix2step35 | -2.908011 | 6.310287 | -2.978958 | 0.0177308 | 0.9998332 | -3.885140 | — | — |
| 191 | ERCCmix2step23 | -2.898560 | 6.773948 | -2.479435 | 0.0382914 | 0.9998332 | -4.060743 | — | — |
| 86 | 47420152_st | -2.702079 | 2.372537 | -3.832384 | 0.0050495 | 0.9998332 | -3.640758 | — | — |
| 176 | ERCC-00014_st | -2.666189 | 9.083521 | -2.620469 | 0.0307616 | 0.9998332 | -4.008866 | — | — |
| 79 | TC10002568.hg.1 | 2.661837 | 5.316601 | 4.009678 | 0.0039380 | 0.9998332 | -3.598487 | — | — |
| 153 | ERCC-00145_st | -2.633929 | 6.178167 | -2.924638 | 0.0192615 | 0.9998332 | -3.903098 | — | — |
| 80 | TC10002567.hg.1 | 2.563995 | 3.893117 | 3.997068 | 0.0040077 | 0.9998332 | -3.601404 | — | — |
| 122 | 47420904_st | 2.541727 | 1.607721 | 3.202307 | 0.0126539 | 0.9998332 | -3.814352 | — | — |
| 8 | 47424360_st | 2.476200 | 2.704951 | 8.838574 | 0.0000219 | 0.1927041 | -3.069890 | — | — |
| 53 | TC01005754.hg.1 | 2.395410 | 6.144722 | 4.872871 | 0.0012538 | 0.9998332 | -3.427984 | — | — |
| 24 | 2985876_st | 2.347245 | 5.731316 | 5.646420 | 0.0004925 | 0.9326515 | -3.315305 | — | — |
| 180 | AFFX-r2-Bs-lys-5_st | -2.337955 | 4.336385 | -2.568832 | 0.0333259 | 0.9998332 | -4.027663 | — | — |
| 75 | TC04000408.hg.1 | 2.196820 | 3.856812 | 4.114278 | 0.0034081 | 0.9998332 | -3.574803 | CXCL8 | chemokine (C-X-C motif) ligand 8 |
| 32 | TC08001612.hg.1 | 2.196815 | 3.636100 | 5.406042 | 0.0006526 | 0.9326515 | -3.346958 | — | — |
| 67 | 47424061_st | 2.181413 | 2.169571 | 4.311166 | 0.0026077 | 0.9998332 | -3.532630 | — | — |
| 195 | TC06003702.hg.1 | 2.159924 | 4.934993 | 2.433458 | 0.0411309 | 0.9998332 | -4.078010 | — | — |
| 234 | 47424282_st | -2.159131 | 4.202975 | -1.815525 | 0.1071746 | 0.9998332 | -4.322302 | — | — |
| 36 | TC01005830.hg.1 | -2.024608 | 4.657497 | -5.219109 | 0.0008168 | 0.9326515 | -3.373569 | FLG | filaggrin |
| 76 | TC02001364.hg.1 | 2.016661 | 2.975513 | 4.103289 | 0.0034599 | 0.9998332 | -3.577249 | CCL20 | chemokine (C-C motif) ligand 20 |
| 31 | 47424232_st | -1.841116 | 1.776524 | -5.445155 | 0.0006230 | 0.9326515 | -3.341617 | — | — |
| 78 | 47421298_st | 1.838922 | 2.238743 | 4.024874 | 0.0038558 | 0.9998332 | -3.594990 | — | — |
| 38 | TC15000024.hg.1 | 1.824639 | 4.616064 | 5.159258 | 0.0008785 | 0.9326515 | -3.382484 | — | — |
| 39 | TC15000148.hg.1 | 1.824639 | 4.616064 | 5.159258 | 0.0008785 | 0.9326515 | -3.382484 | — | — |
| 40 | TC15000207.hg.1 | 1.824639 | 4.616064 | 5.159258 | 0.0008785 | 0.9326515 | -3.382484 | — | — |
| 41 | TC15000238.hg.1 | 1.824639 | 4.616064 | 5.159258 | 0.0008785 | 0.9326515 | -3.382484 | — | — |
| 42 | TC15000243.hg.1 | 1.824639 | 4.616064 | 5.159258 | 0.0008785 | 0.9326515 | -3.382484 | — | — |
| 43 | TC15001014.hg.1 | 1.824639 | 4.616064 | 5.159258 | 0.0008785 | 0.9326515 | -3.382484 | — | — |
| 44 | TC15001053.hg.1 | 1.824639 | 4.616064 | 5.159258 | 0.0008785 | 0.9326515 | -3.382484 | — | — |
| 45 | TC15001115.hg.1 | 1.824639 | 4.616064 | 5.159258 | 0.0008785 | 0.9326515 | -3.382484 | — | — |
| 46 | TC15001129.hg.1 | 1.824639 | 4.616064 | 5.159258 | 0.0008785 | 0.9326515 | -3.382484 | — | — |
| 47 | TC15001157.hg.1 | 1.824639 | 4.616064 | 5.159258 | 0.0008785 | 0.9326515 | -3.382484 | — | — |
| 48 | TC15001673.hg.1 | 1.824639 | 4.616064 | 5.159258 | 0.0008785 | 0.9326515 | -3.382484 | — | — |
| 15 | TC0X001951.hg.1 | 1.818978 | 4.444599 | 7.050275 | 0.0001098 | 0.5164509 | -3.175732 | — | — |
| 72 | 47420665_st | 1.809245 | 2.108061 | 4.148134 | 0.0032534 | 0.9998332 | -3.567331 | — | — |
| 1 | TC6_dbb_hap3000083.hg.1 | 1.736426 | 4.021221 | 11.872761 | 0.0000024 | 0.0436953 | -2.977216 | HLA-DRA | major histocompatibility complex, class II, DR alpha |
| 216 | 47424482_st | 1.678210 | 3.671744 | 2.152784 | 0.0636729 | 0.9998332 | -4.186693 | — | — |
| 6 | TC6_mann_hap4000074.hg.1 | 1.669528 | 4.118256 | 11.221229 | 0.0000037 | 0.0436953 | -2.991608 | HLA-DRA | major histocompatibility complex, class II, DR alpha |
| 3 | TC6_mcf_hap5000075.hg.1 | 1.664986 | 4.117026 | 11.243423 | 0.0000037 | 0.0436953 | -2.991081 | HLA-DRA | major histocompatibility complex, class II, DR alpha |
| 4 | TC6_qbl_hap6000081.hg.1 | 1.664986 | 4.117026 | 11.243423 | 0.0000037 | 0.0436953 | -2.991081 | HLA-DRA | major histocompatibility complex, class II, DR alpha |
| 5 | TC6_ssto_hap7000076.hg.1 | 1.664986 | 4.117026 | 11.243423 | 0.0000037 | 0.0436953 | -2.991081 | HLA-DRA | major histocompatibility complex, class II, DR alpha |
| 2 | TC06000399.hg.1 | 1.660262 | 3.999679 | 11.286359 | 0.0000036 | 0.0436953 | -2.990068 | HLA-DRA | major histocompatibility complex, class II, DR alpha |
| 63 | PSR06024774.hg.1 | -1.648084 | 3.486136 | -4.508144 | 0.0020065 | 0.9998332 | -3.493414 | — | — |
| 247 | 47422444_st | 1.634450 | 2.364348 | 1.318214 | 0.2241037 | 0.9998332 | -4.519889 | — | — |
| 158 | 47423115_st | -1.633955 | 1.950016 | -2.836195 | 0.0220543 | 0.9998332 | -3.932951 | — | — |
| 227 | TC15001625.hg.1 | 1.614497 | 3.258356 | 1.898541 | 0.0943683 | 0.9998332 | -4.288661 | — | — |
| 228 | TC15001677.hg.1 | 1.614497 | 3.258356 | 1.898541 | 0.0943683 | 0.9998332 | -4.288661 | — | — |
| 229 | TC15001844.hg.1 | 1.614497 | 3.258356 | 1.898541 | 0.0943683 | 0.9998332 | -4.288661 | — | — |
| 7 | TC6_cox_hap2000090.hg.1 | 1.580073 | 3.909857 | 9.980765 | 0.0000089 | 0.0899855 | -3.026245 | HLA-DRA | major histocompatibility complex, class II, DR alpha |
| 20 | 47424018_st | -1.577324 | 2.689304 | -5.974953 | 0.0003393 | 0.9326515 | -3.276256 | — | — |
| 231 | 3183417_st | -1.563476 | 3.575752 | -1.881189 | 0.0969183 | 0.9998332 | -4.295687 | — | — |
| 238 | 47422083_st | 1.562201 | 1.894353 | 1.756018 | 0.1173485 | 0.9998332 | -4.346428 | — | — |
| 183 | 3513271_st | -1.559304 | 5.529219 | -2.554673 | 0.0340665 | 0.9998332 | -4.032858 | — | — |
| 187 | TC05001252.hg.1 | 1.553144 | 3.027999 | 2.509408 | 0.0365480 | 0.9998332 | -4.049578 | — | — |
| 188 | TC05001254.hg.1 | 1.553144 | 3.027999 | 2.509408 | 0.0365480 | 0.9998332 | -4.049578 | — | — |
| 25 | TC18000797.hg.1 | 1.543263 | 4.714361 | 5.606665 | 0.0005156 | 0.9326515 | -3.320351 | — | — |
| 119 | TC15000499.hg.1 | -1.539623 | 3.114774 | -3.290014 | 0.0111008 | 0.9998332 | -3.787900 | — | — |
| 11 | TC11003477.hg.1 | 1.528286 | 3.516779 | 7.461492 | 0.0000738 | 0.4731608 | -3.145915 | SAA4 | serum amyloid A4, constitutive |
| 113 | 47420867_st | 1.515104 | 3.250899 | 3.329591 | 0.0104671 | 0.9998332 | -3.776212 | — | — |
| 178 | TC0Y000285.hg.1 | 1.507761 | 5.419692 | 2.586625 | 0.0324185 | 0.9998332 | -4.021160 | — | — |
| 60 | TC16000269.hg.1 | -1.507423 | 3.413260 | -4.559366 | 0.0018761 | 0.9998332 | -3.483679 | — | — |
| 65 | TC08001062.hg.1 | -1.496622 | 5.932169 | -4.475130 | 0.0020957 | 0.9998332 | -3.499787 | STC1 | stanniocalcin 1 |
| 230 | TC05001314.hg.1 | 1.485211 | 4.174103 | 1.888543 | 0.0958297 | 0.9998332 | -4.292709 | — | — |
| 73 | 47421529_st | 1.485158 | 2.093812 | 4.138777 | 0.0032954 | 0.9998332 | -3.569387 | — | — |
| 68 | TC22000577.hg.1 | -1.471848 | 2.949695 | -4.262416 | 0.0027849 | 0.9998332 | -3.542788 | — | — |
| 114 | 47419722_st | -1.469253 | 1.164828 | -3.322254 | 0.0105816 | 0.9998332 | -3.778367 | — | — |
| 9 | 47420725_st | 1.461594 | 2.187253 | 8.014321 | 0.0000444 | 0.3477600 | -3.111522 | — | — |
| 184 | 47422276_st | -1.452694 | 3.611078 | -2.546131 | 0.0345213 | 0.9998332 | -4.036000 | — | — |
| 207 | TC02000729.hg.1 | -1.434884 | 4.516584 | -2.286841 | 0.0516813 | 0.9998332 | -4.134136 | — | — |
| 62 | 47421241_st | 1.434113 | 2.656520 | 4.517065 | 0.0019831 | 0.9998332 | -3.491705 | — | — |
| 168 | 47420903_st | -1.430361 | 3.475447 | -2.658627 | 0.0289969 | 0.9998332 | -3.995128 | — | — |
| 209 | TC0Y000283.hg.1 | 1.421630 | 6.537968 | 2.265508 | 0.0534274 | 0.9998332 | -4.142426 | — | — |
| 30 | TC02001238.hg.1 | -1.411760 | 4.390431 | -5.451950 | 0.0006181 | 0.9326515 | -3.340696 | MAP2 | microtubule-associated protein 2 |
| 169 | TC15002028.hg.1 | 1.399317 | 3.039636 | 2.649006 | 0.0294318 | 0.9998332 | -3.998579 | — | — |
| 170 | TC15002031.hg.1 | 1.399317 | 3.039636 | 2.649006 | 0.0294318 | 0.9998332 | -3.998579 | — | — |
| 171 | TC15002034.hg.1 | 1.399317 | 3.039636 | 2.649006 | 0.0294318 | 0.9998332 | -3.998579 | — | — |
| 172 | TC15002043.hg.1 | 1.399317 | 3.039636 | 2.649006 | 0.0294318 | 0.9998332 | -3.998579 | — | — |
| 173 | TC15002046.hg.1 | 1.399317 | 3.039636 | 2.649006 | 0.0294318 | 0.9998332 | -3.998579 | — | — |
| 174 | TC15002049.hg.1 | 1.399317 | 3.039636 | 2.649006 | 0.0294318 | 0.9998332 | -3.998579 | — | — |
| 12 | TC15001895.hg.1 | -1.396306 | 1.433147 | -7.284620 | 0.0000874 | 0.5125308 | -3.158253 | — | — |
| 66 | 47419884_st | -1.396233 | 1.860523 | -4.404372 | 0.0023019 | 0.9998332 | -3.513715 | — | — |
| 106 | TC6_mcf_hap5000068.hg.1 | -1.390710 | 3.567750 | -3.460219 | 0.0086331 | 0.9998332 | -3.738717 | C4B | complement component 4B (Childo blood group) |
| 221 | TC09000680.hg.1 | 1.373942 | 3.418278 | 2.035254 | 0.0764150 | 0.9998332 | -4.233544 | — | — |
| 192 | 47421410_st | 1.370161 | 2.803220 | 2.476641 | 0.0384582 | 0.9998332 | -4.061787 | — | — |
| 206 | TC05001641.hg.1 | -1.356785 | 4.130772 | -2.297474 | 0.0508324 | 0.9998332 | -4.130014 | SLCO4C1 | solute carrier organic anion transporter family, member 4C1 |
| 115 | TC16000392.hg.1 | 1.341090 | 4.144509 | 3.321701 | 0.0105903 | 0.9998332 | -3.778530 | — | — |
| 116 | TC16001068.hg.1 | 1.341090 | 4.144509 | 3.321701 | 0.0105903 | 0.9998332 | -3.778530 | — | — |
| 34 | 47423221_st | 1.339074 | 1.839781 | 5.336293 | 0.0007092 | 0.9326515 | -3.356674 | — | — |
| 233 | 47420781_st | -1.336553 | 3.242247 | -1.816589 | 0.1070005 | 0.9998332 | -4.321870 | — | — |
| 117 | 47423273_st | -1.320894 | 2.615197 | -3.294196 | 0.0110320 | 0.9998332 | -3.786658 | — | — |
| 218 | 2985916_st | 1.319934 | 2.782601 | 2.138739 | 0.0650785 | 0.9998332 | -4.192258 | — | — |
| 21 | TC11001704.hg.1 | 1.318327 | 1.914391 | 5.935725 | 0.0003545 | 0.9326515 | -3.280681 | — | — |
| 50 | TC12002734.hg.1 | -1.316175 | 10.329069 | -5.119041 | 0.0009229 | 0.9326515 | -3.388586 | SLC2A3 | solute carrier family 2 (facilitated glucose transporter), member 3 |
| 239 | 3371082_st | -1.306390 | 3.515012 | -1.750776 | 0.1182870 | 0.9998332 | -4.348552 | — | — |
| 240 | TC0X001686.hg.1 | 1.305404 | 4.756076 | 1.737273 | 0.1207369 | 0.9998332 | -4.354022 | — | — |
| 69 | TC6_cox_hap2000100.hg.1 | -1.304406 | 2.665726 | -4.252875 | 0.0028211 | 0.9998332 | -3.544797 | HCG24 | HLA complex group 24 |
| 162 | TC01005541.hg.1 | -1.303945 | 3.130221 | -2.747555 | 0.0252758 | 0.9998332 | -3.963621 | — | — |
| 55 | TC20000876.hg.1 | -1.295575 | 8.177874 | -4.740065 | 0.0014846 | 0.9998332 | -3.450785 | SLPI | secretory leukocyte peptidase inhibitor |
| 51 | 47424436_st | -1.280759 | 1.851769 | -5.049985 | 0.0010048 | 0.9383173 | -3.399277 | — | — |
| 161 | 3513255_st | 1.278152 | 3.401479 | 2.773937 | 0.0242692 | 0.9998332 | -3.954415 | — | — |
| 212 | TC0Y000284.hg.1 | 1.277854 | 7.119917 | 2.194625 | 0.0596610 | 0.9998332 | -4.170177 | — | — |
| 226 | 47422029_st | -1.277494 | 4.153074 | -1.943246 | 0.0880916 | 0.9998332 | -4.270585 | — | — |
| 94 | TC0X002222.hg.1 | -1.266617 | 2.816943 | -3.665730 | 0.0064051 | 0.9998332 | -3.683035 | TENM1 | teneurin transmembrane protein 1 |
| 211 | 47420823_st | 1.263319 | 1.972590 | 2.223649 | 0.0570258 | 0.9998332 | -4.158778 | — | — |
| 154 | TC17000752.hg.1 | -1.259876 | 2.522680 | -2.908868 | 0.0197312 | 0.9998332 | -3.908366 | — | — |
| 155 | TC17001046.hg.1 | -1.259876 | 2.522680 | -2.908868 | 0.0197312 | 0.9998332 | -3.908366 | — | — |
| 185 | 47420776_st | -1.254893 | 1.985899 | -2.544224 | 0.0346236 | 0.9998332 | -4.036702 | — | — |
| 143 | 47419808_st | 1.250189 | 2.509886 | 3.007541 | 0.0169766 | 0.9998332 | -3.875806 | — | — |
| 124 | TC18000313.hg.1 | -1.244612 | 2.425847 | -3.131361 | 0.0140769 | 0.9998332 | -3.836303 | — | — |
| 175 | TC13000445.hg.1 | 1.244071 | 2.597201 | 2.629348 | 0.0303414 | 0.9998332 | -4.005657 | — | — |
| 54 | 47424055_st | 1.243592 | 1.433446 | 4.812428 | 0.0013536 | 0.9998332 | -3.438222 | — | — |
| 37 | TC19001622.hg.1 | -1.242909 | 6.488263 | -5.177160 | 0.0008595 | 0.9326515 | -3.379797 | — | — |
| 222 | 47424420_st | 1.230733 | 1.778302 | 1.998546 | 0.0808818 | 0.9998332 | -4.248291 | — | — |
| 81 | TC04000117.hg.1 | -1.228432 | 3.123046 | -3.968485 | 0.0041705 | 0.9998332 | -3.608066 | — | — |
| 139 | 47423852_st | -1.227958 | 1.580189 | -3.081179 | 0.0151841 | 0.9998332 | -3.852131 | — | — |
| 58 | TC02004032.hg.1 | 1.227300 | 5.583444 | 4.608159 | 0.0017603 | 0.9998332 | -3.474577 | — | — |
| 223 | TC15000502.hg.1 | 1.225003 | 3.048121 | 1.997406 | 0.0810244 | 0.9998332 | -4.248749 | — | — |
| 159 | TC12001770.hg.1 | -1.218728 | 3.663200 | -2.819495 | 0.0226271 | 0.9998332 | -3.938673 | — | — |
| 71 | TC06000434.hg.1 | -1.214892 | 3.119678 | -4.194146 | 0.0030553 | 0.9998332 | -3.557324 | — | — |
| 152 | TC15000500.hg.1 | 1.212171 | 3.192299 | 2.933166 | 0.0190124 | 0.9998332 | -3.900260 | — | — |
| 28 | TC12001907.hg.1 | -1.211199 | 6.131961 | -5.486883 | 0.0005931 | 0.9326515 | -3.336002 | — | — |
| 29 | TC12001170.hg.1 | -1.210912 | 9.257128 | -5.460716 | 0.0006117 | 0.9326515 | -3.339513 | SLC2A3 | solute carrier family 2 (facilitated glucose transporter), member 3 |
| 100 | 47421172_st | -1.210637 | 2.636140 | -3.570725 | 0.0073476 | 0.9998332 | -3.708280 | — | — |
| 194 | 47423158_st | 1.210533 | 3.228467 | 2.468320 | 0.0389591 | 0.9998332 | -4.064902 | — | — |
| 27 | 47424102_st | 1.205903 | 1.736368 | 5.491920 | 0.0005896 | 0.9326515 | -3.335330 | — | — |
| 142 | TC22000575.hg.1 | 1.204342 | 3.541077 | 3.053065 | 0.0158439 | 0.9998332 | -3.861107 | — | — |
| 112 | TC02003411.hg.1 | 1.196076 | 4.263230 | 3.344670 | 0.0102358 | 0.9998332 | -3.771799 | — | — |
| 166 | 47422337_st | 1.190992 | 1.346184 | 2.694908 | 0.0274151 | 0.9998332 | -3.982186 | — | — |
| 151 | 47421983_st | -1.190280 | 3.052235 | -2.935904 | 0.0189331 | 0.9998332 | -3.899350 | — | — |
| 84 | TC02003749.hg.1 | -1.188057 | 3.811939 | -3.884024 | 0.0046946 | 0.9998332 | -3.628163 | — | — |
| 157 | 47419750_st | 1.181382 | 1.395260 | 2.872967 | 0.0208454 | 0.9998332 | -3.920447 | — | — |
| 77 | TC09001352.hg.1 | -1.177351 | 1.635598 | -4.041638 | 0.0037672 | 0.9998332 | -3.591154 | — | — |
| 89 | 47422765_st | -1.173435 | 1.462241 | -3.793679 | 0.0053344 | 0.9998332 | -3.650353 | — | — |
| 111 | TC15000519.hg.1 | 1.168808 | 3.695811 | 3.346945 | 0.0102014 | 0.9998332 | -3.771135 | — | — |
| 156 | TC19000891.hg.1 | -1.168794 | 3.308223 | -2.896531 | 0.0201070 | 0.9998332 | -3.912504 | — | — |
| 17 | TC15001710.hg.1 | 1.164777 | 6.540506 | 6.333301 | 0.0002295 | 0.9326515 | -3.238546 | — | — |
| 123 | PSR11017825.hg.1 | -1.161578 | 3.379565 | -3.170057 | 0.0132810 | 0.9998332 | -3.824269 | — | — |
| 91 | 47420572_st | -1.156513 | 2.233184 | -3.716800 | 0.0059525 | 0.9998332 | -3.669811 | — | — |
| 242 | TC09001119.hg.1 | 1.155609 | 2.924916 | 1.622110 | 0.1436315 | 0.9998332 | -4.400528 | — | — |
| 243 | TC09001146.hg.1 | 1.155609 | 2.924916 | 1.622110 | 0.1436315 | 0.9998332 | -4.400528 | — | — |
| 82 | 3662480_st | 1.153765 | 7.158878 | 3.964175 | 0.0041957 | 0.9998332 | -3.609077 | — | — |
| 61 | TC04001997.hg.1 | -1.143170 | 2.702580 | -4.531446 | 0.0019460 | 0.9998332 | -3.488962 | — | — |
| 108 | 47424705_st | 1.141437 | 1.868487 | 3.440236 | 0.0088900 | 0.9998332 | -3.744346 | — | — |
| 196 | PSR02024017.hg.1 | -1.140295 | 7.393396 | -2.409433 | 0.0426983 | 0.9998332 | -4.087099 | — | — |
| 197 | TC12001625.hg.1 | -1.136877 | 6.699157 | -2.401559 | 0.0432250 | 0.9998332 | -4.090087 | DDIT3 | DNA-damage-inducible transcript 3 |
| 13 | TC05001205.hg.1 | 1.134920 | 5.223500 | 7.204022 | 0.0000945 | 0.5125308 | -3.164114 | CDH10 | cadherin 10, type 2 (T2-cadherin) |
| 182 | 3581349_st | 1.133183 | 6.603745 | 2.564882 | 0.0335308 | 0.9998332 | -4.029110 | — | — |
| 200 | 47424739_st | 1.124906 | 1.491184 | 2.363685 | 0.0458511 | 0.9998332 | -4.104525 | — | — |
| 213 | TC03002972.hg.1 | 1.122304 | 6.355611 | 2.190983 | 0.0600000 | 0.9998332 | -4.171611 | — | — |
| 103 | 47424654_st | -1.116210 | 3.976278 | -3.521220 | 0.0078964 | 0.9998332 | -3.721772 | — | — |
| 16 | TC02002499.hg.1 | -1.116043 | 3.027889 | -6.561174 | 0.0001805 | 0.7954087 | -3.216901 | SCN9A | sodium channel, voltage-gated, type IX, alpha subunit |
| 220 | 47423300_st | -1.115688 | 1.597059 | -2.091285 | 0.0700564 | 0.9998332 | -4.211132 | — | — |
| 147 | TC02000836.hg.1 | -1.112505 | 3.744486 | -2.973052 | 0.0178909 | 0.9998332 | -3.887079 | — | — |
| 148 | TC02000839.hg.1 | -1.112505 | 3.744486 | -2.973052 | 0.0178909 | 0.9998332 | -3.887079 | — | — |
| 149 | TC02002312.hg.1 | -1.112505 | 3.744486 | -2.973052 | 0.0178909 | 0.9998332 | -3.887079 | — | — |
| 198 | 47419339_st | -1.111423 | 2.233470 | -2.392681 | 0.0438267 | 0.9998332 | -4.093462 | — | — |
| 186 | TC05002812.hg.1 | -1.104850 | 3.423378 | -2.514053 | 0.0362851 | 0.9998332 | -4.047854 | — | — |
| 202 | TC03001184.hg.1 | -1.102185 | 5.350745 | -2.346722 | 0.0470787 | 0.9998332 | -4.111026 | — | — |
| 248 | TC09002191.hg.1 | 1.101767 | 3.995659 | 1.231122 | 0.2534141 | 0.9998332 | -4.552483 | POLE3 | polymerase (DNA directed), epsilon 3, accessory subunit |
| 101 | TC19002497.hg.1 | -1.099468 | 5.770804 | -3.560899 | 0.0074533 | 0.9998332 | -3.710940 | — | — |
| 205 | 3437243_st | -1.096903 | 2.266081 | -2.308295 | 0.0499828 | 0.9998332 | -4.125828 | — | — |
| 18 | TC08001440.hg.1 | -1.095981 | 4.787639 | -6.190944 | 0.0002676 | 0.9326515 | -3.252962 | TP53INP1 | tumor protein p53 inducible nuclear protein 1 |
| 23 | 47421979_st | -1.094590 | 3.526882 | -5.679526 | 0.0004740 | 0.9326515 | -3.311158 | — | — |
| 102 | TC10000549.hg.1 | 1.093258 | 2.217525 | 3.560801 | 0.0074543 | 0.9998332 | -3.710966 | — | — |
| 237 | 47421387_st | 1.085135 | 2.096303 | 1.774665 | 0.1140667 | 0.9998332 | -4.338870 | — | — |
| 99 | 47423391_st | -1.084978 | 3.603529 | -3.593032 | 0.0071138 | 0.9998332 | -3.702277 | — | — |
| 14 | TC02002628.hg.1 | -1.084255 | 3.832753 | -7.060002 | 0.0001088 | 0.5164509 | -3.174979 | TMEFF2 | transmembrane protein with EGF-like and two follistatin-like domains 2 |
| 193 | TC15001373.hg.1 | 1.082907 | 2.639556 | 2.473446 | 0.0386498 | 0.9998332 | -4.062983 | — | — |
| 208 | TC14000151.hg.1 | -1.081384 | 4.601692 | -2.282042 | 0.0520691 | 0.9998332 | -4.135998 | DHRS2 | dehydrogenase/reductase (SDR family) member 2 |
| 204 | TC11000697.hg.1 | -1.077518 | 6.461707 | -2.314904 | 0.0494708 | 0.9998332 | -4.123275 | ERV9-1 | endogenous retrovirus group 9, member 1 |
| 52 | TC01003245.hg.1 | -1.076095 | 5.883388 | -5.049497 | 0.0010054 | 0.9383173 | -3.399354 | FLG | filaggrin |
| 110 | 47419221_st | 1.073958 | 1.376967 | 3.389999 | 0.0095724 | 0.9998332 | -3.758667 | — | — |
| 56 | 47419283_st | -1.072894 | 1.969319 | -4.630072 | 0.0017109 | 0.9998332 | -3.470543 | — | — |
| 167 | TC15001682.hg.1 | 1.072824 | 3.788845 | 2.686692 | 0.0277654 | 0.9998332 | -3.985106 | FBXO22-AS1 | FBXO22 antisense RNA 1 |
| 224 | 47420802_st | 1.071912 | 1.285461 | 1.992998 | 0.0815785 | 0.9998332 | -4.250523 | — | — |
| 98 | 47420354_st | -1.070933 | 1.896893 | -3.600021 | 0.0070421 | 0.9998332 | -3.700406 | — | — |
| 127 | TC19000688.hg.1 | -1.070164 | 8.395668 | -3.117120 | 0.0143822 | 0.9998332 | -3.840770 | SNAR-A1 | small ILF3/NF90-associated RNA A1 |
| 128 | TC19000689.hg.1 | -1.070164 | 8.395668 | -3.117120 | 0.0143822 | 0.9998332 | -3.840770 | SNAR-A3 | small ILF3/NF90-associated RNA A3 |
| 129 | TC19000691.hg.1 | -1.070164 | 8.395668 | -3.117120 | 0.0143822 | 0.9998332 | -3.840770 | SNAR-A1 | small ILF3/NF90-associated RNA A1 |
| 130 | TC19001731.hg.1 | -1.070164 | 8.395668 | -3.117120 | 0.0143822 | 0.9998332 | -3.840770 | SNAR-A3 | small ILF3/NF90-associated RNA A3 |
| 131 | TC19001732.hg.1 | -1.070164 | 8.395668 | -3.117120 | 0.0143822 | 0.9998332 | -3.840770 | SNAR-A3 | small ILF3/NF90-associated RNA A3 |
| 132 | TC19001733.hg.1 | -1.070164 | 8.395668 | -3.117120 | 0.0143822 | 0.9998332 | -3.840770 | SNAR-A3 | small ILF3/NF90-associated RNA A3 |
| 133 | TC19001734.hg.1 | -1.070164 | 8.395668 | -3.117120 | 0.0143822 | 0.9998332 | -3.840770 | SNAR-A3 | small ILF3/NF90-associated RNA A3 |
| 134 | TC19001735.hg.1 | -1.070164 | 8.395668 | -3.117120 | 0.0143822 | 0.9998332 | -3.840770 | SNAR-A3 | small ILF3/NF90-associated RNA A3 |
| 135 | TC19001736.hg.1 | -1.070164 | 8.395668 | -3.117120 | 0.0143822 | 0.9998332 | -3.840770 | SNAR-A3 | small ILF3/NF90-associated RNA A3 |
| 136 | TC19001737.hg.1 | -1.070164 | 8.395668 | -3.117120 | 0.0143822 | 0.9998332 | -3.840770 | SNAR-A3 | small ILF3/NF90-associated RNA A3 |
| 137 | TC19001738.hg.1 | -1.070164 | 8.395668 | -3.117120 | 0.0143822 | 0.9998332 | -3.840770 | SNAR-A3 | small ILF3/NF90-associated RNA A3 |
| 138 | TC19001739.hg.1 | -1.070164 | 8.395668 | -3.117120 | 0.0143822 | 0.9998332 | -3.840770 | SNAR-A3 | small ILF3/NF90-associated RNA A3 |
| 49 | TC01005829.hg.1 | -1.067675 | 5.425159 | -5.133651 | 0.0009065 | 0.9326515 | -3.386358 | FLG | filaggrin |
| 90 | TC05000701.hg.1 | -1.066769 | 4.695158 | -3.781753 | 0.0054256 | 0.9998332 | -3.653336 | EGR1 | early growth response 1 |
| 181 | PSR05023575.hg.1 | -1.066574 | 7.082133 | -2.567990 | 0.0333695 | 0.9998332 | -4.027971 | — | — |
| 163 | TC15000999.hg.1 | 1.065811 | 4.121194 | 2.746106 | 0.0253324 | 0.9998332 | -3.964129 | DNM1P46 | DNM1 pseudogene 46 |
| 57 | 3671548_st | 1.064946 | 4.824891 | 4.629049 | 0.0017132 | 0.9998332 | -3.470731 | — | — |
| 85 | TC10002574.hg.1 | -1.062514 | 4.520920 | -3.846481 | 0.0049499 | 0.9998332 | -3.637296 | LOC101929397 | uncharacterized LOC101929397 |
| 140 | TC15001883.hg.1 | -1.057253 | 2.032748 | -3.073208 | 0.0153682 | 0.9998332 | -3.854668 | — | — |
| 236 | 47423157_st | -1.052676 | 2.928466 | -1.785013 | 0.1122828 | 0.9998332 | -4.334674 | — | — |
| 35 | TC18000331.hg.1 | 1.051342 | 1.623643 | 5.295141 | 0.0007451 | 0.9326515 | -3.362524 | — | — |
| 104 | TC08000127.hg.1 | -1.050517 | 6.819296 | -3.496742 | 0.0081837 | 0.9998332 | -3.728529 | SLC7A2 | solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 |
| 126 | TC05003066.hg.1 | 1.050114 | 3.051122 | 3.121683 | 0.0142836 | 0.9998332 | -3.839337 | — | — |
| 97 | TC10000516.hg.1 | -1.049653 | 2.268819 | -3.620506 | 0.0068366 | 0.9998332 | -3.694947 | — | — |
| 93 | 47420654_st | -1.049190 | 1.817667 | -3.708997 | 0.0060193 | 0.9998332 | -3.671816 | — | — |
| 95 | TC22000762.hg.1 | -1.048520 | 4.524581 | -3.640090 | 0.0066460 | 0.9998332 | -3.689765 | — | — |
| 64 | TC15000512.hg.1 | -1.048084 | 3.722066 | -4.489440 | 0.0020565 | 0.9998332 | -3.497015 | — | — |
| 210 | TC18000365.hg.1 | 1.046306 | 4.701013 | 2.261539 | 0.0537586 | 0.9998332 | -4.143972 | — | — |
| 219 | 47424344_st | -1.045468 | 1.394740 | -2.121120 | 0.0668847 | 0.9998332 | -4.199253 | — | — |
| 164 | TC12001626.hg.1 | -1.045407 | 3.368001 | -2.704730 | 0.0270023 | 0.9998332 | -3.978703 | MIR616 | microRNA 616 |
| 109 | TC0X001347.hg.1 | -1.044257 | 4.318003 | -3.434510 | 0.0089651 | 0.9998332 | -3.745966 | TENM1 | teneurin transmembrane protein 1 |
| 70 | TC08001816.hg.1 | -1.043123 | 6.020214 | -4.199102 | 0.0030347 | 0.9998332 | -3.556257 | SLC7A2 | solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 |
| 33 | TC13000634.hg.1 | -1.043019 | 5.447627 | -5.371703 | 0.0006798 | 0.9326515 | -3.351710 | SLC25A30 | solute carrier family 25, member 30 |
| 150 | TC15000916.hg.1 | 1.038023 | 4.198438 | 2.938256 | 0.0188653 | 0.9998332 | -3.898569 | — | — |
| 120 | 2985928_st | 1.037305 | 8.521467 | 3.257033 | 0.0116599 | 0.9998332 | -3.797758 | — | — |
| 141 | 2891949_st | -1.037071 | 9.757848 | -3.066503 | 0.0155249 | 0.9998332 | -3.856807 | — | — |
| 244 | TC22000769.hg.1 | -1.036917 | 3.928226 | -1.619180 | 0.1442629 | 0.9998332 | -4.401706 | — | — |
| 246 | 3090545_st | -1.036306 | 3.794809 | -1.469041 | 0.1802049 | 0.9998332 | -4.461504 | — | — |
| 92 | 47423726_st | -1.033061 | 1.926296 | -3.715187 | 0.0059662 | 0.9998332 | -3.670225 | — | — |
| 215 | 47424374_st | 1.030119 | 2.474414 | 2.161769 | 0.0627896 | 0.9998332 | -4.183139 | — | — |
| 203 | TC11001642.hg.1 | 1.029473 | 4.121905 | 2.318557 | 0.0491901 | 0.9998332 | -4.121865 | — | — |
| 160 | 47423074_st | 1.028729 | 1.760860 | 2.785219 | 0.0238514 | 0.9998332 | -3.950499 | — | — |
| 22 | TC06002112.hg.1 | -1.028669 | 6.964645 | -5.889046 | 0.0003735 | 0.9326515 | -3.286027 | CTGF | connective tissue growth factor |
| 96 | 47421498_st | 1.028331 | 2.057299 | 3.631970 | 0.0067243 | 0.9998332 | -3.691909 | — | — |
| 146 | 47419860_st | -1.026830 | 1.828290 | -2.977218 | 0.0177778 | 0.9998332 | -3.885711 | — | — |
| 245 | TC06001355.hg.1 | -1.025945 | 6.777825 | -1.535383 | 0.1634319 | 0.9998332 | -4.435238 | HIST1H4H | histone cluster 1, H4h |
| 118 | 47420668_st | -1.024490 | 2.461771 | -3.294012 | 0.0110350 | 0.9998332 | -3.786712 | — | — |
| 107 | TC19000304.hg.1 | 1.018665 | 2.105424 | 3.448414 | 0.0087839 | 0.9998332 | -3.742037 | — | — |
| 241 | TC07002911.hg.1 | 1.017895 | 2.635082 | 1.670788 | 0.1335040 | 0.9998332 | -4.380912 | — | — |
| 232 | 47420910_st | 1.017542 | 2.138270 | 1.818918 | 0.1066203 | 0.9998332 | -4.320926 | — | — |
| 26 | TC0X000948.hg.1 | -1.017014 | 5.112170 | -5.540506 | 0.0005570 | 0.9326515 | -3.328911 | TMEM47 | transmembrane protein 47 |
| 165 | 47422021_st | -1.015718 | 1.766535 | -2.698662 | 0.0272566 | 0.9998332 | -3.980853 | — | — |
| 144 | 47421855_st | -1.014957 | 1.838986 | -2.987761 | 0.0174949 | 0.9998332 | -3.882257 | — | — |
| 74 | 47419820_st | 1.013300 | 1.448899 | 4.124418 | 0.0033609 | 0.9998332 | -3.572556 | — | — |
| 179 | TC12000135.hg.1 | -1.013162 | 4.926406 | -2.569499 | 0.0332915 | 0.9998332 | -4.027419 | LOC101930011 | uncharacterized LOC101930011 |
| 125 | PSR01009089.hg.1 | -1.011767 | 6.834852 | -3.125101 | 0.0142103 | 0.9998332 | -3.838264 | — | — |
| 19 | TC02000927.hg.1 | -1.009904 | 4.825662 | -6.057611 | 0.0003096 | 0.9326515 | -3.267131 | KIF5C | kinesin family member 5C |
| 59 | TC10000522.hg.1 | -1.009645 | 4.322070 | -4.562917 | 0.0018674 | 0.9998332 | -3.483011 | — | — |
| 214 | TC11002739.hg.1 | -1.007594 | 4.916393 | -2.164929 | 0.0624817 | 0.9998332 | -4.181889 | ERV9-1 | endogenous retrovirus group 9, member 1 |
| 87 | TC15000958.hg.1 | 1.007106 | 4.382472 | 3.795722 | 0.0053189 | 0.9998332 | -3.649843 | — | — |
| 88 | TC15002021.hg.1 | 1.007106 | 4.382472 | 3.795722 | 0.0053189 | 0.9998332 | -3.649843 | — | — |
| 83 | TC16001352.hg.1 | 1.004825 | 2.211975 | 3.902030 | 0.0045772 | 0.9998332 | -3.623827 | — | — |
| 105 | TC18000610.hg.1 | -1.004460 | 6.105710 | -3.493942 | 0.0082172 | 0.9998332 | -3.729305 | — | — |
| 189 | 47422480_st | -1.003643 | 3.676172 | -2.502669 | 0.0369328 | 0.9998332 | -4.052081 | — | — |
| 235 | TC15001418.hg.1 | -1.002835 | 3.315791 | -1.800349 | 0.1096871 | 0.9998332 | -4.328455 | — | — |
| 217 | TC03002590.hg.1 | -1.002169 | 3.980344 | -2.148988 | 0.0640499 | 0.9998332 | -4.188197 | — | — |
| 225 | TC01003326.hg.1 | 1.001183 | 7.807869 | 1.965095 | 0.0851718 | 0.9998332 | -4.261767 | SNORA80E | small nucleolar RNA, H/ACA box 80E |
We have again ~200 DE probes, although MOST of them are not mapped to genes (I don’t know why this is the case, why are there Affymetrix probes with no genes associated?)
over.rep <- read.csv("DE_filtering_testing/logFC.filtering.overrep.tab", sep="\t")
over.rep.simple <- over.rep[c(3,4,5,1,2,6)]
kable(over.rep.simple) %>%
kable_styling() %>%
scroll_box(width = "100%", height = "400px")| pathway | source | external_id | p.value | q.value | members_input_overlap |
|---|---|---|---|---|---|
| Adaptive Immune System | Reactome | R-HSA-1280218 | 0.0031353 | 0.0062706 | FBXO22; DNM1 |
| Immune System | Reactome | R-HSA-168256 | 0.0197630 | 0.0197630 | FBXO22; DNM1 |
While the number of DE genes (or probes) is roughly the same as the non-adjusted p-value list, the pathway mapping is very slight.