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