tdata.FPKM.sample.info <- readRDS(here("Data","20190406_RNAseq_B6_4wk_2DG_counts_phenotypes.RData"))

tdata.FPKM <- readRDS(here("Data","20190406_RNAseq_B6_4wk_2DG_counts_numeric.RData"))

log.tdata.FPKM <- log(tdata.FPKM + 1)
log.tdata.FPKM <- as.data.frame(log.tdata.FPKM)

log.tdata.FPKM.sample.info <- cbind(log.tdata.FPKM, tdata.FPKM.sample.info[,27238:27240])

log.tdata.FPKM.sample.info <- log.tdata.FPKM.sample.info %>% rownames_to_column() %>% filter(rowname != "A113") %>% column_to_rownames()

log.tdata.FPKM.subset <- log.tdata.FPKM[,colMeans(log.tdata.FPKM != 0) > 0.5] 

log.tdata.FPKM.sample.info.subset <- cbind(log.tdata.FPKM.subset,tdata.FPKM.sample.info[,27238:27240])
log.tdata.FPKM.sample.info.subset <- log.tdata.FPKM.sample.info.subset %>% rownames_to_column() %>% filter(rowname != "A113") %>% column_to_rownames()

log.tdata.FPKM.sample.info.subset.SM.SI.spleen <- log.tdata.FPKM.sample.info.subset %>% rownames_to_column() %>% filter(Tissue %in% c("Skeletal Muscle", "Small Intestine", "Spleen")) %>% column_to_rownames()

module.labels <- readRDS(here("Data","SM.SI.spleen","log.tdata.FPKM.sample.info.subset.SM.SI.spleen.WGCNA.module.labels.RData"))

modules <- readRDS(here("Data","SM.SI.spleen","log.tdata.FPKM.sample.info.subset.SM.SI.spleen.WGCNA.module.membership.RData"))

net.deg <- readRDS(here("Data","SM.SI.spleen","Chang_2DG_BL6_connectivity_SM_SI_spleen.RData"))

ensembl.location <- readRDS(here("Data","Ensembl_gene_id_and_location.RData"))

Hub Genes

Hub genes are genes in the module network that have the highest connectivity. For instance, if the gene significance of a particular module is associated with treatment the hub genes in this module are likely associated with this trait.

hub.genes.list <- hub.genes(net.deg,module.labels,modules,ensembl.location)

Turquoise Module

DT.table.hub(hub.genes.list[[1]])

Blue Module

DT.table.hub(hub.genes.list[[2]])

Brown Module

DT.table.hub(hub.genes.list[[3]])

Green Module

DT.table.hub(hub.genes.list[[4]])

ANOVA

To perform analysis of variance Aligned Rank Transformation was performed, which is designed to handle non-parametric multi-factorial experiments. P-value was adjusted using Benjamini-hochberg procedure. Only the top 10 hub genes are listed.

log.tdata.FPKM.sample.info.subset.SM.SI.spleen$Time <- as.factor(log.tdata.FPKM.sample.info.subset.SM.SI.spleen$Time)
log.tdata.FPKM.sample.info.subset.SM.SI.spleen$Treatment <- as.factor(log.tdata.FPKM.sample.info.subset.SM.SI.spleen$Treatment)
log.tdata.FPKM.sample.info.subset.SM.SI.spleen$Tissue <- as.factor(log.tdata.FPKM.sample.info.subset.SM.SI.spleen$Tissue)

for(m in module.labels) {
    name <- str_split(m,"_")[[1]][2]
    hub.met <- net.deg[modules$Gene,] %>%
      dplyr::mutate(Gene=modules$Gene) %>%
      dplyr::filter(modules$Module == m) %>%
      dplyr::arrange(desc(kWithin)) %>%
      dplyr::select(Gene, kWithin)
    gene <- ensembl.location$external_gene_name[match(hub.met$Gene,ensembl.location$ensembl_gene_id)]
    hub.met <- cbind(gene,hub.met)
    cat("\n###",name, "{.tabset .tabset-fade .tabset-pills}","\n")
          for(i in 1:10){
             cat("\n####",hub.met$gene[i],"\n")
             m <- art(data = log.tdata.FPKM.sample.info.subset.SM.SI.spleen, log.tdata.FPKM.sample.info.subset.SM.SI.spleen[,hub.met$Gene[i]] ~ Time*Treatment*Tissue)
             model <- anova(m)
             adjust <- p.adjust(model$`Pr(>F)`, method = "BH")
             print(knitr::kable(cbind(model,adjust)) %>% 
                      column_spec(8, color = "white", background = spec_color(adjust, end = 0.05, scale_from = c(0,0.05))) %>% kable_styling(bootstrap_options = c("striped", "hover", "responsive")))
             cat("\n \n")
             }
          cat("\n \n")
          }

turquoise

Ldb1

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 476.5766 8088.667 2.0621668 0.1598736 0.2797788
Treatment Treatment 1 35 716.4324 7760.500 3.2311237 0.0808835 0.1887281
Tissue Tissue 2 35 7628.6316 946.500 141.0470709 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 1116.2523 7319.667 5.3375148 0.0268867 0.0941035
Time:Tissue Time:Tissue 2 35 152.9211 8236.750 0.3248998 0.7247557 0.7470962
Treatment:Tissue Treatment:Tissue 2 35 135.6771 8075.917 0.2940036 0.7470962 0.7470962
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 690.2166 7483.917 1.6139664 0.2135633 0.2989886

Zbtb5

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 19.47973 8457.7500 0.0806113 0.7781436 0.7781436
Treatment Treatment 1 35 135.19144 8357.9167 0.5661340 0.4568301 0.5329685
Tissue Tissue 2 35 7668.28070 937.6667 143.1157970 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 893.91892 7612.5000 4.1099720 0.0503000 0.1760500
Time:Tissue Time:Tissue 2 35 720.98684 7521.2500 1.6775496 0.2015052 0.4188771
Treatment:Tissue Treatment:Tissue 2 35 495.16447 7642.5000 1.1338408 0.3333298 0.4666618
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 635.33991 7462.9167 1.4898262 0.2393583 0.4188771

Hap1

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 683.7860 7666.4167 3.1217337 0.0859747 0.3009116
Treatment Treatment 1 35 110.0023 8262.9167 0.4659467 0.4993511 0.6990916
Tissue Tissue 2 35 7579.2675 922.9167 143.7152311 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 310.0023 8183.4167 1.3258617 0.2573481 0.5670580
Time:Tissue Time:Tissue 2 35 507.1425 7624.6667 1.1639846 0.3240331 0.5670580
Treatment:Tissue Treatment:Tissue 2 35 151.0724 7961.5000 0.3320689 0.7196735 0.7376145
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 141.1113 8043.9167 0.3069957 0.7376145 0.7376145

Crlf3

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 208.1441 8233.6667 0.8847875 0.3533409 0.4122311
Treatment Treatment 1 35 239.3604 8262.1667 1.0139728 0.3208642 0.4122311
Tissue Tissue 2 35 7648.4386 928.6667 144.1288680 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 1243.3536 7212.4167 6.0336747 0.0191400 0.0669899
Time:Tissue Time:Tissue 2 35 559.5806 7618.0000 1.2854634 0.2892560 0.4122311
Treatment:Tissue Treatment:Tissue 2 35 254.2478 7909.1667 0.5625544 0.5748181 0.5748181
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 549.1952 7463.1667 1.2877798 0.2886325 0.4122311

Lair1

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 951.57658 7521.1667 4.4281933 0.0426023 0.0745540
Treatment Treatment 1 35 1792.03604 6677.1667 9.3933946 0.0041767 0.0097457
Tissue Tissue 2 35 7608.85965 936.1667 142.2343356 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 2256.75901 6167.9167 12.8060364 0.0010358 0.0036254
Time:Tissue Time:Tissue 2 35 755.19737 7526.7500 1.7558646 0.1876346 0.2626884
Treatment:Tissue Treatment:Tissue 2 35 463.78235 7686.4167 1.0559135 0.3586947 0.4184771
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 73.59814 8019.4167 0.1606061 0.8522515 0.8522515

Lpcat2

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 794.6757 7811.500 3.5606028 0.0674830 0.0944762
Treatment Treatment 1 35 871.3604 7658.667 3.9821047 0.0538156 0.0944762
Tissue Tissue 2 35 7628.6316 950.500 140.4535009 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 1047.5766 7481.167 4.9009976 0.0334514 0.0944762
Time:Tissue Time:Tissue 2 35 1095.6162 7336.167 2.6135290 0.0875228 0.1021099
Treatment:Tissue Treatment:Tissue 2 35 1211.0850 6696.917 3.1647381 0.0545309 0.0944762
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 180.7807 7847.167 0.4031598 0.6712686 0.6712686

Apobec3

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 939.9009 7450.1667 4.415543 0.0428823 0.0750439
Treatment Treatment 1 35 569.8401 7844.4167 2.542497 0.1198112 0.1198112
Tissue Tissue 2 35 7618.7412 938.9167 142.001922 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 2110.4144 6149.1667 12.012116 0.0014165 0.0049578
Time:Tissue Time:Tissue 2 35 988.8553 7187.7500 2.407564 0.1047970 0.1198112
Treatment:Tissue Treatment:Tissue 2 35 1932.7412 6214.9167 5.442225 0.0087507 0.0204184
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 932.2149 6658.6667 2.450004 0.1009633 0.1198112

Cdk17

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 236.432432 8361.5000 0.9896711 0.3266511 0.4757863
Treatment Treatment 1 35 1.407658 8572.4167 0.0057473 0.9400013 0.9400013
Tissue Tissue 2 35 7608.859649 943.1667 141.1787000 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 654.326577 7911.4167 2.8947319 0.0977387 0.2280569
Time:Tissue Time:Tissue 2 35 1828.609649 6547.4167 4.8875259 0.0134295 0.0470032
Treatment:Tissue Treatment:Tissue 2 35 500.986842 7875.5000 1.1132334 0.3398474 0.4757863
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 264.539474 7981.7500 0.5800032 0.5651868 0.6593846

Rad9a

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 140.7658 8412.667 0.5856409 0.4492396 0.4492396
Treatment Treatment 1 35 2002.8131 6602.417 10.6170908 0.0024952 0.0087332
Tissue Tissue 2 35 7658.3553 927.750 144.4583316 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 818.9392 7785.250 3.6816893 0.0631979 0.1474617
Time:Tissue Time:Tissue 2 35 789.4271 7493.917 1.8434918 0.1733028 0.3032799
Treatment:Tissue Treatment:Tissue 2 35 530.5307 7705.417 1.2049040 0.3118494 0.3638243
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 628.3224 7518.750 1.4624295 0.2454829 0.3436761

Cyb561a3

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 1977.4077 6325.9167 10.9405912 0.0021840 0.0050960
Treatment Treatment 1 35 264.9752 8120.4167 1.1420760 0.2925296 0.4095414
Tissue Tissue 2 35 7648.4386 937.1667 142.8216348 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 2830.2725 5407.4167 18.3191983 0.0001378 0.0004824
Time:Tissue Time:Tissue 2 35 373.7675 7651.9167 0.8548096 0.4340531 0.5063953
Treatment:Tissue Treatment:Tissue 2 35 908.4057 7218.6667 2.2022211 0.1256464 0.2198812
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 135.0175 7691.9167 0.3071805 0.7374805 0.7374805

blue

Hn1l

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 781.3536 7781.917 3.5142211 0.0692095 0.1837890
Treatment Treatment 1 35 165.4077 8418.917 0.6876500 0.4125848 0.5776188
Tissue Tissue 2 35 7626.4803 978.250 136.4307739 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 212.2725 8325.917 0.8923388 0.3513202 0.5776188
Time:Tissue Time:Tissue 2 35 1094.3306 7002.000 2.7350450 0.0787667 0.1837890
Treatment:Tissue Treatment:Tissue 2 35 218.3613 7703.667 0.4960395 0.6131538 0.7153462
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 115.7961 7878.500 0.2572102 0.7746543 0.7746543

Tes

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 2185.1914 6251.917 12.233320 0.0012974 0.0030272
Treatment Treatment 1 35 996.0023 7557.917 4.612393 0.0387458 0.0542441
Tissue Tissue 2 35 7628.6316 943.000 141.570575 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 3210.8919 5357.000 20.978386 0.0000566 0.0001981
Time:Tissue Time:Tissue 2 35 2178.5395 5439.250 7.009136 0.0027538 0.0048191
Treatment:Tissue Treatment:Tissue 2 35 687.7566 6775.250 1.776428 0.1841625 0.2148563
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 478.0280 6540.500 1.279029 0.2909953 0.2909953

Kras

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 729.191441 7851.4167 3.2505854 0.0800137 0.1400240
Treatment Treatment 1 35 1.407658 8559.9167 0.0057557 0.9399576 0.9399576
Tissue Tissue 2 35 7618.741228 951.9167 140.0626506 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 1240.009009 7303.1667 5.9426708 0.0199983 0.0466626
Time:Tissue Time:Tissue 2 35 2151.809211 5985.2500 6.2915770 0.0046319 0.0162117
Treatment:Tissue Treatment:Tissue 2 35 519.813597 7420.1667 1.2259479 0.3057730 0.4280822
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 102.609649 7693.9167 0.2333881 0.7930686 0.9252467

Nipsnap3b

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 879.7860 7696.417 4.0008893 0.0532825 0.0932445
Treatment Treatment 1 35 1138.5608 7479.250 5.3280247 0.0270135 0.0630314
Tissue Tissue 2 35 7598.9868 931.250 142.7997527 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 1592.9752 7002.417 7.9621273 0.0078211 0.0273739
Time:Tissue Time:Tissue 2 35 471.4583 7505.167 1.0993121 0.3443265 0.4820570
Treatment:Tissue Treatment:Tissue 2 35 232.7516 7739.750 0.5262643 0.5954092 0.6021124
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 224.2166 7622.917 0.5147360 0.6021124 0.6021124

Erlin2

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 263.432432 8314.0000 1.1089891 0.2995180 0.6344859
Treatment Treatment 1 35 7.576577 8603.1667 0.0308236 0.8616464 0.8616464
Tissue Tissue 2 35 7638.530702 952.9167 140.2790947 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 668.975225 7911.9167 2.9593503 0.0942139 0.3297487
Time:Tissue Time:Tissue 2 35 460.657895 7717.7500 1.0445419 0.3625634 0.6344859
Treatment:Tissue Treatment:Tissue 2 35 320.808662 7921.9167 0.7086860 0.4992180 0.6989052
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 141.111294 7959.6667 0.3102451 0.7352629 0.8578067

Mapk1ip1l

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 213.65766 8245.167 0.9069578 0.3474539 0.6080443
Treatment Treatment 1 35 117.08108 8438.500 0.4856121 0.4904941 0.6866917
Tissue Tissue 2 35 7598.98684 946.750 140.4618640 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 32.43243 8471.500 0.1339946 0.7165291 0.7565629
Time:Tissue Time:Tissue 2 35 816.77632 6743.750 2.1195308 0.1352431 0.3895963
Treatment:Tissue Treatment:Tissue 2 35 123.65789 7695.500 0.2812050 0.7565629 0.7565629
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 759.46491 7051.917 1.8846842 0.1669699 0.3895963

Ezr

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 1547.84009 7000.9167 7.7381871 0.0086506 0.0302771
Treatment Treatment 1 35 65.09009 8400.1667 0.2712033 0.6058050 0.6058050
Tissue Tissue 2 35 7579.26754 920.4167 144.1055848 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 215.04730 8251.2500 0.9121837 0.3460862 0.4845206
Time:Tissue Time:Tissue 2 35 1298.13322 6560.2500 3.4628759 0.0424400 0.0990268
Treatment:Tissue Treatment:Tissue 2 35 379.62445 7638.4167 0.8697389 0.4279211 0.4992412
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 471.03070 7293.1667 1.1302412 0.3344587 0.4845206

Galk2

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 2211.8941 6192.9167 12.500781 0.0011674 0.0040859
Treatment Treatment 1 35 590.4144 7994.1667 2.584948 0.1168690 0.1636166
Tissue Tissue 2 35 7579.2675 933.4167 142.098579 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 1994.3266 6449.9167 10.822067 0.0022929 0.0053501
Time:Tissue Time:Tissue 2 35 635.1245 6952.4167 1.598678 0.2165748 0.2526706
Treatment:Tissue Treatment:Tissue 2 35 461.3701 7514.0000 1.074524 0.3524569 0.3524569
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 1621.0016 6544.0000 4.334891 0.0207981 0.0363966

Eno3

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 792.00225 7818.4167 3.5454850 0.0680404 0.1587609
Treatment Treatment 1 35 193.35360 8362.4167 0.8092608 0.3744868 0.5242815
Tissue Tissue 2 35 7618.74123 953.9167 139.7689926 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 816.22523 7774.1667 3.6747196 0.0634361 0.1587609
Time:Tissue Time:Tissue 2 35 544.50439 7201.6667 1.3231419 0.2792890 0.4887557
Treatment:Tissue Treatment:Tissue 2 35 103.18421 7565.0000 0.2386945 0.7889272 0.8117504
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 90.44518 7543.9167 0.2098102 0.8117504 0.8117504

Ppip5k2

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 2036.93919 6446.250 11.0595884 0.0020802 0.0072806
Treatment Treatment 1 35 22.97523 8522.917 0.0943495 0.7605391 0.7605391
Tissue Tissue 2 35 7604.78070 1012.667 131.4190213 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 1752.08108 6683.500 9.1752581 0.0045875 0.0107042
Time:Tissue Time:Tissue 2 35 1251.45833 6735.167 3.2516672 0.0506685 0.0886700
Treatment:Tissue Treatment:Tissue 2 35 254.67708 7958.917 0.5599819 0.5762526 0.7100109
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 220.96656 7676.417 0.5037396 0.6085808 0.7100109

brown

Cldn23

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 1138.56081 7095.75 5.6159854 0.0234409 0.0820432
Treatment Treatment 1 35 386.02703 7799.00 1.7323947 0.1966607 0.3441561
Tissue Tissue 2 35 6211.54112 2013.00 53.9999849 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 426.18243 7806.75 1.9107036 0.1756433 0.3441561
Time:Tissue Time:Tissue 2 35 439.86184 7068.50 1.0889980 0.3476852 0.4867593
Treatment:Tissue Treatment:Tissue 2 35 19.12007 7717.50 0.0433562 0.9576216 0.9576216
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 128.88322 7219.75 0.3124009 0.7337072 0.8559917

Ttc22

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 1170.8131 7192.917 5.6970571 0.0225303 0.0398284
Treatment Treatment 1 35 2380.1441 5758.167 14.4672862 0.0005488 0.0019209
Tissue Tissue 2 35 5779.6579 2528.000 40.0094989 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 1032.2725 6364.917 5.6763568 0.0227591 0.0398284
Time:Tissue Time:Tissue 2 35 353.5833 6476.167 0.9554585 0.3944402 0.4601802
Treatment:Tissue Treatment:Tissue 2 35 676.3087 5753.667 2.0570190 0.1430110 0.2002154
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 91.6886 6758.167 0.2374239 0.7899167 0.7899167

Arhgef16

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 563.06306 7977.167 2.4704520 0.1250021 0.2187536
Treatment Treatment 1 35 818.93919 7715.250 3.7150930 0.0620697 0.1448294
Tissue Tissue 2 35 6281.90789 2275.750 48.3064432 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 990.02027 7550.250 4.5893460 0.0392066 0.1372232
Time:Tissue Time:Tissue 2 35 456.52796 7679.500 1.0403333 0.3640064 0.5096089
Treatment:Tissue Treatment:Tissue 2 35 210.41393 7942.917 0.4635884 0.6328295 0.7383011
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 66.16447 8061.000 0.1436395 0.8667079 0.8667079

Gucy2c

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 140.76577 8217.167 0.5995743 0.4439400 0.6215160
Treatment Treatment 1 35 1712.57658 6714.167 8.9274192 0.0051073 0.0178755
Tissue Tissue 2 35 6539.52796 1976.500 57.9012089 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 1187.10811 6576.500 6.3177653 0.0167076 0.0389844
Time:Tissue Time:Tissue 2 35 24.08991 7680.917 0.0548858 0.9466745 0.9466745
Treatment:Tissue Treatment:Tissue 2 35 739.39254 6686.917 1.9350278 0.1595605 0.2792309
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 63.46491 7475.417 0.1485718 0.8624788 0.9466745

Sgpp2

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 1840.5766 6631.667 9.714026 0.0036428 0.0127500
Treatment Treatment 1 35 1380.8311 6865.250 7.039669 0.0119066 0.0166692
Tissue Tissue 2 35 5920.5411 2214.000 46.797412 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 1380.8311 6480.250 7.457905 0.0098245 0.0166692
Time:Tissue Time:Tissue 2 35 1747.4534 5810.917 5.262584 0.0100413 0.0166692
Treatment:Tissue Treatment:Tissue 2 35 421.9846 6700.667 1.102089 0.3434281 0.3434281
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 1182.4583 6277.917 3.296161 0.0488046 0.0569387

Cgn

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 698.7590090 7708.917 3.1725035 0.0835682 0.1949924
Treatment Treatment 1 35 0.8130631 8378.417 0.0033965 0.9538575 0.9976008
Tissue Tissue 2 35 6607.3481360 1949.917 59.2992482 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 1148.1891892 6978.500 5.7586332 0.0218644 0.0765254
Time:Tissue Time:Tissue 2 35 872.9868421 7007.750 2.1800535 0.1281463 0.2242560
Treatment:Tissue Treatment:Tissue 2 35 1.0981360 7999.917 0.0024022 0.9976008 0.9976008
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 197.2516447 7586.500 0.4550061 0.6381439 0.8934014

Esrp1

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 438.0203 7033.75 2.1795926 0.1487928 0.2603874
Treatment Treatment 1 35 1935.4257 6292.75 10.7647529 0.0023476 0.0082167
Tissue Tissue 2 35 6263.1332 1515.50 72.3225545 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 301.7027 7140.50 1.4788313 0.2320958 0.3249341
Time:Tissue Time:Tissue 2 35 372.2368 6749.50 0.9651300 0.3908404 0.4559804
Treatment:Tissue Treatment:Tissue 2 35 1505.1332 5743.50 4.5860244 0.0170258 0.0397270
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 273.0592 7119.50 0.6711899 0.5175555 0.5175555

Mpzl2

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 287.0473 8105.750 1.2394480 0.2731653 0.4780392
Treatment Treatment 1 35 46.7027 8257.500 0.1979527 0.6591179 0.6591179
Tissue Tissue 2 35 7005.1645 1546.500 79.2695624 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 478.6509 7921.417 2.1148719 0.1547839 0.3611625
Time:Tissue Time:Tissue 2 35 1578.1332 6657.750 4.1481479 0.0241715 0.0846001
Treatment:Tissue Treatment:Tissue 2 35 314.8481 7804.167 0.7060129 0.5005023 0.5839193
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 342.8481 7763.417 0.7728353 0.4694203 0.5839193

Dsp

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 315.03604 7573.167 1.4559644 0.2356659 0.3009696
Treatment Treatment 1 35 1943.78604 6465.917 10.5217117 0.0025957 0.0090851
Tissue Tissue 2 35 6099.33498 2267.667 47.0696878 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 874.16441 6914.917 4.4246021 0.0426816 0.0995904
Time:Tissue Time:Tissue 2 35 77.03235 7100.917 0.1898439 0.8279342 0.8279342
Treatment:Tissue Treatment:Tissue 2 35 1019.76480 6619.000 2.6961602 0.0814633 0.1425607
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 561.12939 6970.667 1.4087267 0.2579740 0.3009696

Cdh1

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 8.657658 8253.667 0.0367131 0.8491576 0.8491576
Treatment Treatment 1 35 616.056306 7784.917 2.7697112 0.1049927 0.3674745
Tissue Tissue 2 35 7138.320175 1394.417 89.5862808 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 274.326577 7839.917 1.2246852 0.2759915 0.4829851
Time:Tissue Time:Tissue 2 35 198.616228 7673.667 0.4529496 0.6394243 0.7459951
Treatment:Tissue Treatment:Tissue 2 35 573.234649 7293.167 1.3754802 0.2660423 0.4829851
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 439.447368 7258.000 1.0595659 0.3574614 0.5004459

green

Slc16a9

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 6.567568 8468.0000 0.0271451 0.8700825 0.8920454
Treatment Treatment 1 35 194.675676 8366.5000 0.8143965 0.3729925 0.8419293
Tissue Tissue 2 35 7688.017544 941.6667 142.8746623 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 668.975225 7946.9167 2.9463166 0.0949131 0.3321958
Time:Tissue Time:Tissue 2 35 243.848136 8270.1667 0.5159923 0.6013780 0.8419293
Treatment:Tissue Treatment:Tissue 2 35 55.142544 8419.6667 0.1146120 0.8920454 0.8920454
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 301.171053 8239.5000 0.6396618 0.5335254 0.8419293

Slc6a8

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 71.360360 8490.1667 0.2941771 0.5909931 0.8273904
Treatment Treatment 1 35 1.191441 8574.4167 0.0048634 0.9447993 0.9448106
Tissue Tissue 2 35 7688.004386 955.9167 140.7445664 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 1.191441 8577.9167 0.0048614 0.9448106 0.9448106
Time:Tissue Time:Tissue 2 35 420.449013 8148.5000 0.9029708 0.4145978 0.8182421
Treatment:Tissue Treatment:Tissue 2 35 416.883224 8159.7500 0.8940784 0.4181193 0.8182421
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 365.570175 8233.9167 0.7769666 0.4675669 0.8182421

Stab2

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 426.1824324 8033.2500 1.8568307 0.1816952 0.3179666
Treatment Treatment 1 35 440.0090090 7949.6667 1.9372278 0.1727524 0.3179666
Tissue Tissue 2 35 7688.0043860 934.9167 143.9059561 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 0.0563063 8352.4167 0.0002359 0.9878318 0.9878318
Time:Tissue Time:Tissue 2 35 1265.9013158 7287.7500 3.0397960 0.0606364 0.2122275
Treatment:Tissue Treatment:Tissue 2 35 232.8700658 8112.0000 0.5023701 0.6093914 0.7109567
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 299.9473684 8047.2500 0.6522823 0.5270711 0.7109567

Slc9a2

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 7.84009 8574.417 0.0320025 0.8590536 0.8590536
Treatment Treatment 1 35 321.81081 8236.000 1.3675787 0.2501310 0.3501834
Tissue Tissue 2 35 7688.03947 950.750 141.5100613 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 342.56757 8187.500 1.4644110 0.2343393 0.3501834
Time:Tissue Time:Tissue 2 35 660.40570 7892.667 1.4642833 0.2450633 0.3501834
Treatment:Tissue Treatment:Tissue 2 35 1713.76754 6816.667 4.3996477 0.0197477 0.0691169
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 195.78235 8412.167 0.4072900 0.6685643 0.7799917

Tcp11l2

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 1233.33333 7305.667 5.9086554 0.0203297 0.0711540
Treatment Treatment 1 35 363.97297 8094.500 1.5737913 0.2179706 0.3683891
Tissue Tissue 2 35 7688.00000 953.500 141.1012061 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 303.35360 8208.417 1.2934743 0.2631351 0.3683891
Time:Tissue Time:Tissue 2 35 23.60526 8532.750 0.0484125 0.9528043 0.9528043
Treatment:Tissue Treatment:Tissue 2 35 994.83333 7501.667 2.3207621 0.1131253 0.2639590
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 226.62281 8259.667 0.4801524 0.6227043 0.7264884

Parp8

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 797.35360 7207.417 3.8720359 0.0570607 0.1997124
Treatment Treatment 1 35 29.78604 7989.917 0.1304784 0.7201079 0.7201079
Tissue Tissue 2 35 7363.80866 1237.417 104.1416809 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 38.65090 7884.917 0.1715657 0.6812516 0.7201079
Time:Tissue Time:Tissue 2 35 391.36129 7670.167 0.8929171 0.4185816 0.7201079
Treatment:Tissue Treatment:Tissue 2 35 190.50164 7740.250 0.4307069 0.6534482 0.7201079
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 379.90132 7354.250 0.9040042 0.4141905 0.7201079

Nin

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 499.6418919 7860.7500 2.2246562 0.1447819 0.3721499
Treatment Treatment 1 35 328.6576577 8194.1667 1.4038057 0.2440705 0.3721499
Tissue Tissue 2 35 7626.9846491 965.9167 138.1819322 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 0.0022523 8345.4167 0.0000094 0.9975652 0.9975652
Time:Tissue Time:Tissue 2 35 332.2368421 8060.7500 0.7212908 0.4932089 0.5754104
Treatment:Tissue Treatment:Tissue 2 35 605.2516447 7695.5000 1.3763763 0.2658214 0.3721499
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 694.2823465 7614.9167 1.5955448 0.2171975 0.3721499

Cst6

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 190.72297 8239.7500 0.8101343 0.3742321 0.6497827
Treatment Treatment 1 35 71.36036 8394.6667 0.2975237 0.5888986 0.6870484
Tissue Tissue 2 35 7688.00439 924.4167 145.5405139 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 19.47973 8430.2500 0.0808743 0.7777919 0.7777919
Time:Tissue Time:Tissue 2 35 587.45340 7747.6667 1.3269072 0.2783131 0.6493973
Treatment:Tissue Treatment:Tissue 2 35 362.54112 8085.5000 0.7846725 0.4641305 0.6497827
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 1563.11129 6759.9167 4.0465658 0.0262452 0.0918582

Fbp2

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 1122.6036036 6751.6667 5.8194707 0.0212274 0.0495306
Treatment Treatment 1 35 0.7297297 7950.5000 0.0032124 0.9551237 0.9551237
Tissue Tissue 2 35 7688.0701754 873.1667 154.0842467 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 1017.0810811 6860.5000 5.1888110 0.0289498 0.0506622
Time:Tissue Time:Tissue 2 35 2118.6557018 5804.9167 6.3870813 0.0043183 0.0151140
Treatment:Tissue Treatment:Tissue 2 35 88.7149123 7775.4167 0.1996692 0.8199281 0.9551237
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 125.4057018 7723.6667 0.2841396 0.7543811 0.9551237

Cep170

Term Df Df.res Sum Sq Sum Sq.res F value Pr(>F) adjust
Time Time 1 35 592.72297 7964.250 2.6048032 0.1155214 0.4043251
Treatment Treatment 1 35 365.78604 8140.917 1.5726130 0.2181392 0.4570550
Tissue Tissue 2 35 7626.48026 1011.000 132.0112805 0.0000000 0.0000000
Time:Treatment Time:Treatment 1 35 13.00901 8518.167 0.0534523 0.8185077 0.8185077
Time:Tissue Time:Tissue 2 35 631.90132 7924.750 1.3954097 0.2611743 0.4570550
Treatment:Tissue Treatment:Tissue 2 35 422.09375 8024.250 0.9205397 0.4077319 0.4756873
Time:Treatment:Tissue Time:Treatment:Tissue 2 35 508.90132 7937.750 1.1219518 0.3370737 0.4719032

Analysis performed by Ann Wells

The Carter Lab The Jackson Laboratory 2023

ann.wells@jax.org