Comparisons with other data sets
ERM
2023-05-31
Last updated: 2023-05-31
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Knit directory: Cardiotoxicity/
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’
Data set comparison order:
Knowles data: meQTLS(aka K4 supp) meQTLS(aka K4 supp)
#Pairwise Data enrichment ## Knowles Comparison data:
Determining the genetic basis of anthracycline-cardiotoxicity by molecular response QTL mapping in induced cardiomyocytes David A Knowles, Courtney K Burrows†, John D Blischak, Kristen M Patterson, Daniel J Serie, Nadine Norton, Carole Ober, Jonathan K Pritchard, Yoav Gilad
Knowles \(~~et~ al.~\) eLife 2018;7:e33480. DOI: https://doi.org/10.7554/eLife.33480 My first question was about transcription response at the 24 hour mark with my treatments. 3 hour RNA-seq had low levels of DEGs,so my focus is at 24 hours. This also happens to be when the Knowles paper collected their RNA-seq data
Supplementary 4 contains a list of 518 SNPs within 1 Mb of TSS, which had a detectable marginal effect on expression (5% FDR). When converted from ensembl gene id to entrez gene id, my list of unique Entrezgeneids = 521. I will call these meSNPs for marginal effect snps. In the meSNPs, 503 are within my DEG of 14084. Using an adj. P value of 0.05, There are 199/6864 in 24 hour daunorubicin, 184/6516 in 24 hour doxorubicin, 182/6202 in 24 hour epirubicin, 30/1327 in 24 hour mitoxantrone and 0 in Trastuzumb
Supplementary 5 contains a list of 376 response eQTLs (reQTLs). These are variants that were associated with modulation of transcriptomic response to doxorubicin treatment. After database name conversion, I have 377 unique Entregene ids. Of the reQTLs list, 374 are within my DEG of 14084. Using an adj. P value of 0.05, There are 187/6864 in 24 hour daunorubicin, 180/6516 in 24 hour doxorubicin, 176/6202 in 24 hour epirubicin, 40/1327 in 24 hour mitoxantrone and 0 in Trastuzumb.
| time | id | n | K4 | K5 |
|---|---|---|---|---|
| 24_hours | Daunorubicin | 6864 | 199 | 187 |
| 24_hours | Doxorubicin | 6516 | 184 | 180 |
| 24_hours | Epirubicin | 6202 | 172 | 176 |
| 24_hours | Mitoxantrone | 1327 | 30 | 40 |
| time | id | n | K4 | K5 |
|---|---|---|---|---|
| 24_hours | Daunorubicin | 14084 | 503 | 374 |
| 24_hours | Doxorubicin | 14084 | 503 | 374 |
| 24_hours | Epirubicin | 14084 | 503 | 374 |
| 24_hours | Mitoxantrone | 14084 | 503 | 374 |
| 24_hours | Trastuzumab | 14084 | 503 | 374 |
[1] "this is the meSNPs (mininmally expressed QTLS)"# A tibble: 8 × 3
# Groups: id [4]
id time pvalue
<fct> <chr> <dbl>
1 Daunorubicin 24_hours 0.0000338
2 Daunorubicin 3_hours 0.00188
3 Doxorubicin 24_hours 0.0000113
4 Doxorubicin 3_hours 0.923
5 Epirubicin 24_hours 0.00000740
6 Epirubicin 3_hours 0.219
7 Mitoxantrone 24_hours 0.00865
8 Mitoxantrone 3_hours 0.685 [1] "below is the reQTLS in knowles data ( reQTLS)"# A tibble: 8 × 3
# Groups: id [4]
id time pvalue
<fct> <chr> <dbl>
1 Daunorubicin 24_hours 0.658
2 Daunorubicin 3_hours 0.739
3 Doxorubicin 24_hours 0.497
4 Doxorubicin 3_hours 1.00
5 Epirubicin 24_hours 0.254
6 Epirubicin 3_hours 0.571
7 Mitoxantrone 24_hours 0.445
8 Mitoxantrone 3_hours 0.395
ArrGWAS to 24 hour DEG genes p < 0.05
24 hour data set
| id | sigcount | ARR | ARRcount |
|---|---|---|---|
| Daunorubicin | notsig | no | 7169 |
| Daunorubicin | notsig | y | 51 |
| Daunorubicin | sig | no | 6795 |
| Daunorubicin | sig | y | 69 |
| Doxorubicin | notsig | no | 7512 |
| Doxorubicin | notsig | y | 56 |
| Doxorubicin | sig | no | 6452 |
| Doxorubicin | sig | y | 64 |
| Epirubicin | notsig | no | 7827 |
| Epirubicin | notsig | y | 55 |
| Epirubicin | sig | no | 6137 |
| Epirubicin | sig | y | 65 |
| Mitoxantrone | notsig | no | 12650 |
| Mitoxantrone | notsig | y | 107 |
| Mitoxantrone | sig | no | 1314 |
| Mitoxantrone | sig | y | 13 |
| Trastuzumab | notsig | no | 13964 |
| Trastuzumab | notsig | y | 120 |
3 hour data set
| id | sigcount | ARR | ARRcount |
|---|---|---|---|
| Daunorubicin | notsig | no | 7169 |
| Daunorubicin | notsig | y | 51 |
| Daunorubicin | sig | no | 6795 |
| Daunorubicin | sig | y | 69 |
| Doxorubicin | notsig | no | 7512 |
| Doxorubicin | notsig | y | 56 |
| Doxorubicin | sig | no | 6452 |
| Doxorubicin | sig | y | 64 |
| Epirubicin | notsig | no | 7827 |
| Epirubicin | notsig | y | 55 |
| Epirubicin | sig | no | 6137 |
| Epirubicin | sig | y | 65 |
| Mitoxantrone | notsig | no | 12650 |
| Mitoxantrone | notsig | y | 107 |
| Mitoxantrone | sig | no | 1314 |
| Mitoxantrone | sig | y | 13 |
| Trastuzumab | notsig | no | 13964 |
| Trastuzumab | notsig | y | 120 |
chi square test ARR
chi_funarr <- toplistall %>%
mutate(id = as.factor(id)) %>%
dplyr::filter(id!="Trastuzumab") %>%
mutate(sigcount = if_else(adj.P.Val <0.05,'sig','notsig'))%>%
mutate(ARR=if_else(ENTREZID %in%Arr_geneset$entrezgene_id,"y","no")) %>%
group_by(id,time) %>%
summarise(pvalue= chisq.test(ARR, sigcount)$p.value)
print("after performing chi square test between DEgenes, and non DE genes")[1] "after performing chi square test between DEgenes, and non DE genes"chi_funarr# A tibble: 8 × 3
# Groups: id [4]
id time pvalue
<fct> <chr> <dbl>
1 Daunorubicin 24_hours 0.0662
2 Daunorubicin 3_hours 0.0246
3 Doxorubicin 24_hours 0.142
4 Doxorubicin 3_hours 1.00
5 Epirubicin 24_hours 0.0313
6 Epirubicin 3_hours 0.644
7 Mitoxantrone 24_hours 0.708
8 Mitoxantrone 3_hours 0.00409HFGWAS
24 hours HF
| id | sigcount | HF | HFcount |
|---|---|---|---|
| Daunorubicin | notsig | no | 7209 |
| Daunorubicin | notsig | y | 11 |
| Daunorubicin | sig | no | 6842 |
| Daunorubicin | sig | y | 22 |
| Doxorubicin | notsig | no | 7556 |
| Doxorubicin | notsig | y | 12 |
| Doxorubicin | sig | no | 6495 |
| Doxorubicin | sig | y | 21 |
| Epirubicin | notsig | no | 7868 |
| Epirubicin | notsig | y | 14 |
| Epirubicin | sig | no | 6183 |
| Epirubicin | sig | y | 19 |
| Mitoxantrone | notsig | no | 12728 |
| Mitoxantrone | notsig | y | 29 |
| Mitoxantrone | sig | no | 1323 |
| Mitoxantrone | sig | y | 4 |
| Trastuzumab | notsig | no | 14051 |
| Trastuzumab | notsig | y | 33 |
3 hours HF
| id | sigcount | HF | HFcount |
|---|---|---|---|
| Daunorubicin | notsig | no | 13498 |
| Daunorubicin | notsig | y | 31 |
| Daunorubicin | sig | no | 553 |
| Daunorubicin | sig | y | 2 |
| Doxorubicin | notsig | no | 14035 |
| Doxorubicin | notsig | y | 33 |
| Doxorubicin | sig | no | 16 |
| Epirubicin | notsig | no | 13831 |
| Epirubicin | notsig | y | 33 |
| Epirubicin | sig | no | 220 |
| Mitoxantrone | notsig | no | 13993 |
| Mitoxantrone | notsig | y | 33 |
| Mitoxantrone | sig | no | 58 |
| Trastuzumab | notsig | no | 14051 |
| Trastuzumab | notsig | y | 33 |
chi square test HF
chi_funhf <- toplistall %>%
mutate(id = as.factor(id)) %>%
dplyr::filter(id!="Trastuzumab") %>%
mutate(sigcount = if_else(adj.P.Val <0.05,'sig','notsig'))%>%
mutate(HF=if_else(ENTREZID %in%HF_geneset$entrezgene_id,"y","no")) %>%
group_by(id,time) %>%
summarise(pvalue= chisq.test(HF, sigcount)$p.value)
print("after performing chi square test between DEgenes, and non DE genes")[1] "after performing chi square test between DEgenes, and non DE genes"chi_funhf# A tibble: 8 × 3
# Groups: id [4]
id time pvalue
<fct> <chr> <dbl>
1 Daunorubicin 24_hours 0.0589
2 Daunorubicin 3_hours 0.858
3 Doxorubicin 24_hours 0.0674
4 Doxorubicin 3_hours 1.00
5 Epirubicin 24_hours 0.164
6 Epirubicin 3_hours 0.983
7 Mitoxantrone 24_hours 0.816
8 Mitoxantrone 3_hours 1.00 CAD GWAS
24 hour data set
| id | sigcount | CAD | CADcount |
|---|---|---|---|
| Daunorubicin | notsig | no | 7107 |
| Daunorubicin | notsig | y | 113 |
| Daunorubicin | sig | no | 6748 |
| Daunorubicin | sig | y | 116 |
| Doxorubicin | notsig | no | 7447 |
| Doxorubicin | notsig | y | 121 |
| Doxorubicin | sig | no | 6408 |
| Doxorubicin | sig | y | 108 |
| Epirubicin | notsig | no | 7762 |
| Epirubicin | notsig | y | 120 |
| Epirubicin | sig | no | 6093 |
| Epirubicin | sig | y | 109 |
| Mitoxantrone | notsig | no | 12547 |
| Mitoxantrone | notsig | y | 210 |
| Mitoxantrone | sig | no | 1308 |
| Mitoxantrone | sig | y | 19 |
| Trastuzumab | notsig | no | 13855 |
| Trastuzumab | notsig | y | 229 |
3 hour data set
| id | sigcount | CAD | CADcount |
|---|---|---|---|
| Daunorubicin | notsig | no | 13317 |
| Daunorubicin | notsig | y | 212 |
| Daunorubicin | sig | no | 538 |
| Daunorubicin | sig | y | 17 |
| Doxorubicin | notsig | no | 13839 |
| Doxorubicin | notsig | y | 229 |
| Doxorubicin | sig | no | 16 |
| Epirubicin | notsig | no | 13643 |
| Epirubicin | notsig | y | 221 |
| Epirubicin | sig | no | 212 |
| Epirubicin | sig | y | 8 |
| Mitoxantrone | notsig | no | 13798 |
| Mitoxantrone | notsig | y | 228 |
| Mitoxantrone | sig | no | 57 |
| Mitoxantrone | sig | y | 1 |
| Trastuzumab | notsig | no | 13855 |
| Trastuzumab | notsig | y | 229 |
chi square test CAD
chi_funCAD <- toplistall %>%
mutate(id = as.factor(id)) %>%
dplyr::filter(id!="Trastuzumab") %>%
mutate(sigcount = if_else(adj.P.Val <0.05,'sig','notsig'))%>%
mutate(CAD=if_else(ENTREZID %in%CAD_geneset$entrezgene_id,"y","no")) %>%
group_by(id,time) %>%
summarise(pvalue= chisq.test(CAD, sigcount)$p.value)
print("after performing chi square test between DEgenes, and non DE genes")[1] "after performing chi square test between DEgenes, and non DE genes"chi_funCAD# A tibble: 8 × 3
# Groups: id [4]
id time pvalue
<fct> <chr> <dbl>
1 Daunorubicin 24_hours 0.604
2 Daunorubicin 3_hours 0.0105
3 Doxorubicin 24_hours 0.836
4 Doxorubicin 3_hours 1.00
5 Epirubicin 24_hours 0.304
6 Epirubicin 3_hours 0.0351
7 Mitoxantrone 24_hours 0.636
8 Mitoxantrone 3_hours 1.00 GTEx V8 heart-left ventrical egenes
####chi square
| id | time | sigcount | no | y |
|---|---|---|---|---|
| Daunorubicin | 24_hours | notsig | 866 | 6354 |
| Daunorubicin | 24_hours | sig | 797 | 6067 |
| Daunorubicin | 3_hours | notsig | 1628 | 11901 |
| Daunorubicin | 3_hours | sig | 35 | 520 |
| Doxorubicin | 24_hours | notsig | 920 | 6648 |
| Doxorubicin | 24_hours | sig | 743 | 5773 |
| Doxorubicin | 3_hours | notsig | 1662 | 12406 |
| Doxorubicin | 3_hours | sig | 1 | 15 |
| Epirubicin | 24_hours | notsig | 953 | 6929 |
| Epirubicin | 24_hours | sig | 710 | 5492 |
| Epirubicin | 3_hours | notsig | 1651 | 12213 |
| Epirubicin | 3_hours | sig | 12 | 208 |
| Mitoxantrone | 24_hours | notsig | 1503 | 11254 |
| Mitoxantrone | 24_hours | sig | 160 | 1167 |
| Mitoxantrone | 3_hours | notsig | 1660 | 12366 |
| Mitoxantrone | 3_hours | sig | 3 | 55 |
| Trastuzumab | 24_hours | notsig | 1663 | 12421 |
| Trastuzumab | 3_hours | notsig | 1663 | 12421 |
[1] "after performing chi square test between DEgenes, and non DE genes"# A tibble: 8 × 3
# Groups: id [4]
id time pvalue
<fct> <chr> <dbl>
1 Daunorubicin 24_hours 0.498
2 Daunorubicin 3_hours 0.0000556
3 Doxorubicin 24_hours 0.175
4 Doxorubicin 3_hours 0.763
5 Epirubicin 24_hours 0.251
6 Epirubicin 3_hours 0.00454
7 Mitoxantrone 24_hours 0.802
8 Mitoxantrone 3_hours 0.172 Seaone 2019
Seoane, Jose Chromatin gene comparison: comes from supp data NAT. MED 2019 ### 24 hours in Pairwise with supplemental data 1
| id | notsig_no | notsig_y | sig_no | sig_y |
|---|---|---|---|---|
| Daunorubicin | 7065 | 155 | 6689 | 175 |
| Doxorubicin | 7407 | 161 | 6347 | 169 |
| Epirubicin | 7717 | 165 | 6037 | 165 |
| Mitoxantrone | 12483 | 274 | 1271 | 56 |
| Trastuzumab | 13754 | 330 | NA | NA |
# A tibble: 4 × 2
id pvalue
<fct> <dbl>
1 Daunorubicin 0.128
2 Doxorubicin 0.0771
3 Epirubicin 0.0314
4 Mitoxantrone 0.000003263 hours data Pairwise
| id | notsig_no | notsig_y | sig_no | sig_y |
|---|---|---|---|---|
| Daunorubicin | 13227 | 302 | 527 | 28 |
| Doxorubicin | 13738 | 330 | 16 | NA |
| Epirubicin | 13551 | 313 | 203 | 17 |
| Mitoxantrone | 13698 | 328 | 56 | 2 |
| Trastuzumab | 13754 | 330 | NA | NA |
chi square test Seaone
##remove Trastuzumab in order to perform chi square tests by time and drug between DE and non DE enrichment
chi_fun <- toplistall %>%
mutate(id = as.factor(id)) %>%
dplyr::filter(id!="Trastuzumab") %>%
mutate(sigcount = if_else(adj.P.Val <0.05,'sig','notsig'))%>%
mutate(chrom=if_else(ENTREZID %in%chrom_genes,"y","no")) %>%
group_by(id,time) %>%
summarise(pvalue= chisq.test(chrom, sigcount)$p.value)
print("after performing chi square test between DEgenes, and non DE genes")[1] "after performing chi square test between DEgenes, and non DE genes"chi_fun# A tibble: 8 × 3
# Groups: id [4]
id time pvalue
<fct> <chr> <dbl>
1 Daunorubicin 24_hours 0.128
2 Daunorubicin 3_hours 0.0000332
3 Doxorubicin 24_hours 0.0771
4 Doxorubicin 3_hours 1.00
5 Epirubicin 24_hours 0.0314
6 Epirubicin 3_hours 0.000000346
7 Mitoxantrone 24_hours 0.00000326
8 Mitoxantrone 3_hours 0.902 Supplemental 4 Seoane 3 hours followed by 24 hours
| entrez | gene | pval.exp | pval.anthr | pval.expAnth | adjpval |
|---|---|---|---|---|---|
| 11176 | BAZ2A | 0.0020064 | 0.0000768 | 0.0004553 | 0.1299006 |
| 10284 | SAP18 | 0.0013141 | 0.0000648 | 0.0006081 | 0.1299006 |
| 8819 | SAP30 | 0.0023742 | 0.0000576 | 0.0007455 | 0.1299006 |
| 23522 | KAT6B | 0.0050327 | 0.0001601 | 0.0012776 | 0.1343691 |
| 7786 | MAP3K12 | 0.0062822 | 0.0001296 | 0.0014816 | 0.1343691 |
| 2146 | EZH2 | 0.0075650 | 0.0001626 | 0.0020478 | 0.1343691 |
| 4297 | KMT2A | 0.0096126 | 0.0001301 | 0.0023292 | 0.1343691 |
| 79913 | ACTR5 | 0.0087568 | 0.0001883 | 0.0035210 | 0.1373866 |
| 8242 | KDM5C | 0.0139853 | 0.0001783 | 0.0036176 | 0.1373866 |
| 51780 | KDM3B | 0.0155602 | 0.0001675 | 0.0039239 | 0.1373866 |
| 6872 | TAF1 | 0.0105527 | 0.0001952 | 0.0043619 | 0.1447734 |
| 23135 | KDM6B | 0.0074796 | 0.0001950 | 0.0047811 | 0.1514738 |
| 6877 | TAF5 | 0.0233826 | 0.0002047 | 0.0067329 | 0.1624738 |
| 23030 | KDM4B | 0.0239951 | 0.0004270 | 0.0069023 | 0.1624738 |
| 64324 | NSD1 | 0.0164702 | 0.0003839 | 0.0069286 | 0.1624738 |
| 79885 | HDAC11 | 0.0256039 | 0.0002383 | 0.0071964 | 0.1624738 |
| 10847 | SRCAP | 0.0174738 | 0.0003660 | 0.0077132 | 0.1624738 |
| 7404 | UTY | 0.0114041 | 0.0002112 | 0.0078450 | 0.1624738 |
| 51773 | RSF1 | 0.0283587 | 0.0001948 | 0.0080182 | 0.1624738 |
| 5253 | PHF2 | 0.0119978 | 0.0002989 | 0.0093089 | 0.1624738 |
| 9126 | SMC3 | 0.0347884 | 0.0002127 | 0.0095907 | 0.1624738 |
| 3054 | HCFC1 | 0.0317868 | 0.0003159 | 0.0097354 | 0.1624738 |
| 9734 | HDAC9 | 0.0353794 | 0.0001985 | 0.0103307 | 0.1649465 |
| 53335 | BCL11A | 0.0063102 | 0.0004723 | 0.0105391 | 0.1649465 |
| 83444 | INO80B | 0.0255912 | 0.0003477 | 0.0112276 | 0.1701220 |
| 27350 | APOBEC3C | 0.0051330 | 0.0004220 | 0.0122160 | 0.1745980 |
| 6601 | SMARCC2 | 0.0336512 | 0.0003435 | 0.0122745 | 0.1745980 |
| 1108 | CHD4 | 0.0238388 | 0.0003994 | 0.0127656 | 0.1778779 |
| 8289 | ARID1A | 0.0492112 | 0.0004149 | 0.0146053 | 0.1870798 |
| 890 | CCNA2 | 0.0444477 | 0.0004539 | 0.0147624 | 0.1870798 |
| 64151 | NCAPG | 0.0003946 | 0.0003956 | 0.0154184 | 0.1919043 |
| 10445 | MCRS1 | 0.0185317 | 0.0003143 | 0.0162352 | 0.1977683 |
| 7150 | TOP1 | 0.0468031 | 0.0003256 | 0.0175446 | 0.2072644 |
| 8110 | DPF3 | 0.0612773 | 0.0004235 | 0.0182917 | 0.2124890 |
| 54531 | MIER2 | 0.0244962 | 0.0004771 | 0.0198964 | 0.2273412 |
| 51409 | HEMK1 | 0.0718548 | 0.0004890 | 0.0223436 | 0.2395917 |
| 27097 | TAF5L | 0.0450661 | 0.0003586 | 0.0237889 | 0.2512251 |
| 9739 | SETD1A | 0.0590016 | 0.0005136 | 0.0245980 | 0.2558930 |
| 6595 | SMARCA2 | 0.0491644 | 0.0005485 | 0.0267793 | 0.2645703 |
| 9555 | H2AFY | 0.0852250 | 0.0004323 | 0.0277200 | 0.2645703 |
| 22823 | MTF2 | 0.0823105 | 0.0005160 | 0.0278843 | 0.2645703 |
| 54556 | ING3 | 0.0701823 | 0.0004542 | 0.0280892 | 0.2645703 |
| 10592 | SMC2 | 0.0788583 | 0.0006366 | 0.0286097 | 0.2658792 |
| 8360 | HIST1H4D | 0.0801302 | 0.0004891 | 0.0300157 | 0.2715200 |
| 7528 | YY1 | 0.1017709 | 0.0005254 | 0.0342873 | 0.2836505 |
| 9031 | BAZ1B | 0.1069563 | 0.0005045 | 0.0354054 | 0.2836505 |
| 51377 | UCHL5 | 0.1048249 | 0.0005627 | 0.0372967 | 0.2954064 |
| 7799 | PRDM2 | 0.0130131 | 0.0006154 | 0.0382200 | 0.2993182 |
| 6602 | SMARCD1 | 0.1110653 | 0.0006993 | 0.0446426 | 0.3241241 |
| 8202 | NCOA3 | 0.1179716 | 0.0006899 | 0.0454845 | 0.3251323 |
| 51564 | HDAC7 | 0.1331938 | 0.0007507 | 0.0463305 | 0.3251323 |
| 26038 | CHD5 | 0.0624026 | 0.0005717 | 0.0477023 | 0.3265622 |
| 79858 | NEK11 | 0.1358428 | 0.0006363 | 0.0490482 | 0.3265622 |
| 10856 | RUVBL2 | 0.1277997 | 0.0007652 | 0.0498579 | 0.3278390 |
| 56950 | SMYD2 | 0.1018914 | 0.0005905 | 0.0518406 | 0.3309161 |
| 23081 | KDM4C | 0.1535477 | 0.0006316 | 0.0532858 | 0.3316091 |
| 5252 | PHF1 | 0.0589957 | 0.0009403 | 0.0555393 | 0.3368815 |
| 10013 | HDAC6 | 0.1508016 | 0.0007079 | 0.0565497 | 0.3368815 |
| 605 | BCL7A | 0.1751811 | 0.0007178 | 0.0624106 | 0.3655476 |
| 57680 | CHD8 | 0.1404978 | 0.0008216 | 0.0641107 | 0.3689294 |
| 1786 | DNMT1 | 0.0742639 | 0.0010553 | 0.0645759 | 0.3689294 |
| 8932 | MBD2 | 0.0413684 | 0.0006937 | 0.0670724 | 0.3720616 |
| 7703 | PCGF2 | 0.1080288 | 0.0008390 | 0.0672593 | 0.3720616 |
| 387893 | SETD8 | 0.0325632 | 0.0009001 | 0.0686467 | 0.3767463 |
| 580 | BARD1 | 0.1608293 | 0.0008545 | 0.0703017 | 0.3780927 |
| 10274 | STAG1 | 0.1947375 | 0.0007542 | 0.0705194 | 0.3780927 |
| 22992 | KDM2A | 0.0895616 | 0.0008314 | 0.0721146 | 0.3785189 |
| 23133 | PHF8 | 0.1967192 | 0.0007999 | 0.0721911 | 0.3785189 |
| 2122 | MECOM | 0.1604149 | 0.0005958 | 0.0738655 | 0.3819777 |
| 10014 | HDAC5 | 0.2023646 | 0.0008066 | 0.0739842 | 0.3819777 |
| 3065 | HDAC1 | 0.1594520 | 0.0008370 | 0.0756461 | 0.3832878 |
| 5978 | REST | 0.1957721 | 0.0010360 | 0.0804648 | 0.3900125 |
| 3012 | HIST1H2AE | 0.1401041 | 0.0007383 | 0.0809965 | 0.3900125 |
| 5580 | PRKCD | 0.0509785 | 0.0008470 | 0.0816956 | 0.3900125 |
| 3014 | H2AFX | 0.2039117 | 0.0009085 | 0.0874291 | 0.4029968 |
| 3070 | HELLS | 0.2103033 | 0.0009403 | 0.0883885 | 0.4029968 |
| 8986 | RPS6KA4 | 0.2439747 | 0.0009272 | 0.0946755 | 0.4193677 |
| 9437 | NCR1 | 0.1757248 | 0.0008247 | 0.0961261 | 0.4193677 |
| 10765 | KDM5B | 0.1822552 | 0.0009461 | 0.0962681 | 0.4193677 |
| 8726 | EED | 0.2536795 | 0.0009473 | 0.1022474 | 0.4392490 |
| 8193 | DPF1 | 0.1617765 | 0.0009552 | 0.1027225 | 0.4392490 |
| 5926 | ARID4A | 0.2046667 | 0.0009423 | 0.1051371 | 0.4441245 |
| 54892 | NCAPG2 | 0.2719518 | 0.0009517 | 0.1128685 | 0.4611639 |
| 8940 | TOP3B | 0.2249933 | 0.0010145 | 0.1133632 | 0.4611639 |
| 8846 | ALKBH1 | 0.2036862 | 0.0009869 | 0.1135440 | 0.4611639 |
| 3010 | HIST1H1T | 0.2667468 | 0.0011193 | 0.1144639 | 0.4611639 |
| 1106 | CHD2 | 0.2880572 | 0.0010542 | 0.1174722 | 0.4667835 |
| 8208 | CHAF1B | 0.1937594 | 0.0009776 | 0.1202905 | 0.4667835 |
| 10362 | HMG20B | 0.1361831 | 0.0012375 | 0.1262857 | 0.4815909 |
| 9112 | MTA1 | 0.1427047 | 0.0009402 | 0.1279681 | 0.4821284 |
| 9085 | CDY1 | 0.3218780 | 0.0009130 | 0.1329480 | 0.4907047 |
| 94239 | H2AFV | 0.3003611 | 0.0012008 | 0.1387756 | 0.5090874 |
| 6881 | TAF10 | 0.3189882 | 0.0011176 | 0.1399581 | 0.5103299 |
| 23210 | JMJD6 | 0.0919038 | 0.0007698 | 0.1413109 | 0.5103299 |
| 6594 | SMARCA1 | 0.1546347 | 0.0009547 | 0.1437595 | 0.5150159 |
| 8363 | HIST1H4J | 0.3520914 | 0.0011282 | 0.1508657 | 0.5257670 |
| 84148 | KAT8 | 0.2983520 | 0.0011745 | 0.1549367 | 0.5293672 |
| 29781 | NCAPH2 | 0.3655076 | 0.0010676 | 0.1562522 | 0.5312574 |
| 8353 | HIST1H3E | 0.1915487 | 0.0012986 | 0.1581816 | 0.5346205 |
| 55729 | ATF7IP | 0.2948714 | 0.0013894 | 0.1682765 | 0.5558707 |
| 983 | CDK1 | 0.0629620 | 0.0013244 | 0.1718000 | 0.5637297 |
| 8085 | KMT2D | 0.0700734 | 0.0013433 | 0.1722732 | 0.5637297 |
| 29947 | DNMT3L | 0.3907083 | 0.0011692 | 0.1741601 | 0.5672412 |
| 8341 | HIST1H2BN | 0.3038599 | 0.0012809 | 0.1756827 | 0.5695389 |
| 54904 | WHSC1L1 | 0.2716103 | 0.0011647 | 0.1804500 | 0.5796020 |
| 2648 | KAT2A | 0.4161649 | 0.0013730 | 0.1855535 | 0.5841609 |
| 8314 | BAP1 | 0.3409185 | 0.0011776 | 0.1876702 | 0.5841609 |
| 7156 | TOP3A | 0.4236425 | 0.0012461 | 0.1903988 | 0.5872035 |
| 79903 | NAA60 | 0.4195751 | 0.0011239 | 0.1929107 | 0.5923293 |
| 8520 | HAT1 | 0.4012166 | 0.0011749 | 0.1967219 | 0.5948079 |
| 8850 | KAT2B | 0.2666902 | 0.0011467 | 0.1994806 | 0.5948079 |
| 60 | ACTB | 0.4095978 | 0.0012664 | 0.2013874 | 0.5948079 |
| 9682 | KDM4A | 0.0481174 | 0.0015790 | 0.2017269 | 0.5948079 |
| 23186 | RCOR1 | 0.4301622 | 0.0011904 | 0.2022517 | 0.5948079 |
| 3020 | H3F3A | 0.2045507 | 0.0013618 | 0.2060137 | 0.5962376 |
| 6760 | SS18 | 0.4294569 | 0.0013025 | 0.2109426 | 0.6050494 |
| 8358 | HIST1H3B | 0.4201442 | 0.0012949 | 0.2151399 | 0.6136120 |
| 25855 | BRMS1 | 0.4468722 | 0.0012664 | 0.2169290 | 0.6136120 |
| 3066 | HDAC2 | 0.4660358 | 0.0012886 | 0.2183377 | 0.6136120 |
| 3015 | H2AFZ | 0.0874045 | 0.0013310 | 0.2207807 | 0.6136120 |
| 1107 | CHD3 | 0.1755650 | 0.0013172 | 0.2213914 | 0.6136120 |
| 5885 | RAD21 | 0.4212044 | 0.0012773 | 0.2220577 | 0.6136120 |
| 23067 | SETD1B | 0.4112018 | 0.0012331 | 0.2227261 | 0.6136120 |
| 8369 | HIST1H4G | 0.0541162 | 0.0012376 | 0.2257280 | 0.6141468 |
| 8464 | SUPT3H | 0.1407375 | 0.0016483 | 0.2269937 | 0.6141468 |
| 1387 | CREBBP | 0.3879121 | 0.0012180 | 0.2372847 | 0.6229271 |
| 6597 | SMARCA4 | 0.4942178 | 0.0012715 | 0.2418715 | 0.6229271 |
| 7403 | KDM6A | 0.2449474 | 0.0016652 | 0.2421998 | 0.6229271 |
| 6599 | SMARCC1 | 0.4398084 | 0.0013837 | 0.2434911 | 0.6239459 |
| 55818 | KDM3A | 0.4796703 | 0.0013475 | 0.2453545 | 0.6244196 |
| 4221 | MEN1 | 0.1602106 | 0.0015565 | 0.2474853 | 0.6257047 |
| 8354 | HIST1H3I | 0.2038803 | 0.0013008 | 0.2566278 | 0.6427487 |
| 64919 | BCL11B | 0.3397001 | 0.0013853 | 0.2572176 | 0.6427487 |
| 2778 | GNAS | 0.5313339 | 0.0013673 | 0.2607783 | 0.6486002 |
| 23063 | WAPAL | 0.4803188 | 0.0014101 | 0.2640332 | 0.6486002 |
| 10474 | TADA3 | 0.4182951 | 0.0012877 | 0.2646696 | 0.6486002 |
| 5925 | RB1 | 0.0180124 | 0.0013884 | 0.2654438 | 0.6486002 |
| 8352 | HIST1H3C | 0.5101982 | 0.0013060 | 0.2699923 | 0.6486002 |
| 23047 | PDS5B | 0.4115119 | 0.0012520 | 0.2737249 | 0.6486002 |
| 10629 | TAF6L | 0.0816771 | 0.0019828 | 0.2760177 | 0.6486002 |
| 9985 | REC8 | 0.1586687 | 0.0018821 | 0.2763251 | 0.6486002 |
| 79068 | FTO | 0.5262576 | 0.0015592 | 0.2766267 | 0.6486002 |
| 22933 | SIRT2 | 0.4597759 | 0.0016624 | 0.2771808 | 0.6486002 |
| 79831 | KDM8 | 0.4677240 | 0.0012925 | 0.2784008 | 0.6486002 |
| 23244 | PDS5A | 0.1845290 | 0.0013872 | 0.2785362 | 0.6486002 |
| 53615 | MBD3 | 0.5558590 | 0.0014806 | 0.2804021 | 0.6493032 |
| 2145 | EZH1 | 0.1060722 | 0.0020869 | 0.2910505 | 0.6673804 |
| 6944 | VPS72 | 0.4682202 | 0.0014221 | 0.2942899 | 0.6681434 |
| 11143 | KAT7 | 0.5797010 | 0.0013508 | 0.2965725 | 0.6689678 |
| 10051 | SMC4 | 0.4276521 | 0.0013049 | 0.3022513 | 0.6717176 |
| 8284 | KDM5D | 0.5865781 | 0.0013536 | 0.3027745 | 0.6717176 |
| 1105 | CHD1 | 0.0562306 | 0.0013912 | 0.3031303 | 0.6717176 |
| 51412 | ACTL6B | 0.0221382 | 0.0021366 | 0.3045909 | 0.6718349 |
| 9575 | CLOCK | 0.3073567 | 0.0019029 | 0.3103947 | 0.6781978 |
| 546 | ATRX | 0.1651338 | 0.0015736 | 0.3115867 | 0.6786748 |
| 55274 | PHF10 | 0.4525002 | 0.0017498 | 0.3131804 | 0.6800210 |
| 171023 | ASXL1 | 0.6120455 | 0.0015709 | 0.3287267 | 0.6931019 |
| 51111 | SUV420H1 | 0.4922838 | 0.0015531 | 0.3321552 | 0.6973258 |
| 63976 | PRDM16 | 0.5048752 | 0.0014079 | 0.3413291 | 0.7059537 |
| 7468 | WHSC1 | 0.3778328 | 0.0014712 | 0.3453368 | 0.7100287 |
| 51742 | ARID4B | 0.3576952 | 0.0013925 | 0.3464448 | 0.7102118 |
| 9862 | MED24 | 0.5470702 | 0.0015288 | 0.3503800 | 0.7119968 |
| 23310 | NCAPD3 | 0.6477900 | 0.0016613 | 0.3530529 | 0.7151499 |
| 8330 | HIST1H2AK | 0.5342719 | 0.0014776 | 0.3544273 | 0.7151499 |
| 65980 | BRD9 | 0.3009104 | 0.0017701 | 0.3601637 | 0.7183265 |
| 9757 | KMT2B | 0.5925410 | 0.0016623 | 0.3611372 | 0.7183265 |
| 23411 | SIRT1 | 0.0187646 | 0.0019759 | 0.3661747 | 0.7250675 |
| 10930 | APOBEC2 | 0.6220587 | 0.0015421 | 0.3686738 | 0.7266228 |
| 7994 | KAT6A | 0.6671120 | 0.0015130 | 0.3690451 | 0.7266228 |
| 84159 | ARID5B | 0.4855813 | 0.0014913 | 0.3711648 | 0.7277438 |
| 7153 | TOP2A | 0.0050316 | 0.0007244 | 0.3717027 | 0.7277438 |
| 472 | ATM | 0.5440090 | 0.0015634 | 0.3732830 | 0.7287907 |
| 9918 | NCAPD2 | 0.6144771 | 0.0020164 | 0.3777089 | 0.7353718 |
| 1788 | DNMT3A | 0.1278948 | 0.0014916 | 0.3805218 | 0.7387846 |
| 339 | APOBEC1 | 0.5149224 | 0.0014329 | 0.3906825 | 0.7501384 |
| 9913 | SUPT7L | 0.5899114 | 0.0015518 | 0.3908648 | 0.7501384 |
| 11177 | BAZ1A | 0.1380176 | 0.0016418 | 0.3934506 | 0.7511128 |
| 86 | ACTL6A | 0.4151123 | 0.0015856 | 0.3944151 | 0.7511128 |
| 6015 | RING1 | 0.1908945 | 0.0020119 | 0.3987402 | 0.7514971 |
| 8648 | NCOA1 | 0.4412936 | 0.0016790 | 0.3994943 | 0.7514971 |
| 57379 | AICDA | 0.1088297 | 0.0016494 | 0.4000078 | 0.7514971 |
| 6605 | SMARCE1 | 0.0593302 | 0.0008522 | 0.4083211 | 0.7587234 |
| 2033 | EP300 | 0.4087541 | 0.0017250 | 0.4092930 | 0.7587234 |
| 10042 | HMGXB4 | 0.5989112 | 0.0016359 | 0.4213236 | 0.7587234 |
| 8493 | PPM1D | 0.2754904 | 0.0017428 | 0.4231774 | 0.7587234 |
| 55193 | PBRM1 | 0.4636168 | 0.0013669 | 0.4237488 | 0.7587234 |
| 55636 | CHD7 | 0.5530869 | 0.0015638 | 0.4266136 | 0.7587234 |
| 80012 | PHC3 | 0.4454474 | 0.0017710 | 0.4302145 | 0.7587234 |
| 1017 | CDK2 | 0.6040736 | 0.0016532 | 0.4344865 | 0.7587234 |
| 8089 | YEATS4 | 0.6796301 | 0.0015984 | 0.4370231 | 0.7587234 |
| 8243 | SMC1A | 0.0511580 | 0.0016305 | 0.4370911 | 0.7587234 |
| 85236 | HIST1H2BK | 0.6323675 | 0.0014129 | 0.4389658 | 0.7587234 |
| 54145 | H2BFS | 0.6015056 | 0.0014664 | 0.4390000 | 0.7587234 |
| 79813 | EHMT1 | 0.6604409 | 0.0015757 | 0.4410421 | 0.7587234 |
| 23492 | CBX7 | 0.1290072 | 0.0021702 | 0.4430422 | 0.7587234 |
| 23309 | SIN3B | 0.2406406 | 0.0017645 | 0.4511831 | 0.7662102 |
| 10919 | EHMT2 | 0.7371111 | 0.0017541 | 0.4569279 | 0.7662102 |
| 5931 | RBBP7 | 0.1589186 | 0.0019033 | 0.4602643 | 0.7662102 |
| 55870 | ASH1L | 0.1526004 | 0.0016161 | 0.4631444 | 0.7662102 |
| 8841 | HDAC3 | 0.1869212 | 0.0019228 | 0.4645445 | 0.7662102 |
| 5977 | DPF2 | 0.0306372 | 0.0019654 | 0.4693999 | 0.7662102 |
| 8359 | HIST1H4A | 0.7614716 | 0.0016568 | 0.4708443 | 0.7663836 |
| 23512 | SUZ12 | 0.4344670 | 0.0014710 | 0.4747729 | 0.7669624 |
| 6419 | SETMAR | 0.7561483 | 0.0016581 | 0.4759176 | 0.7669624 |
| 8535 | CBX4 | 0.7280592 | 0.0018291 | 0.4764630 | 0.7669624 |
| 3017 | HIST1H2BD | 0.7819131 | 0.0016560 | 0.4835593 | 0.7730294 |
| 200316 | APOBEC3F | 0.3982946 | 0.0011894 | 0.4887242 | 0.7794984 |
| 6603 | SMARCD2 | 0.7900836 | 0.0016116 | 0.4960757 | 0.7876191 |
| 54815 | GATAD2A | 0.4127019 | 0.0019824 | 0.5029724 | 0.7961341 |
| 8331 | HIST1H2AJ | 0.5990501 | 0.0015006 | 0.5102847 | 0.8028633 |
| 84193 | SETD3 | 0.7132852 | 0.0015549 | 0.5134659 | 0.8060490 |
| 9252 | RPS6KA5 | 0.7349994 | 0.0018791 | 0.5212601 | 0.8127927 |
| 9070 | ASH2L | 0.7763350 | 0.0016710 | 0.5328165 | 0.8222253 |
| 8970 | HIST1H2BJ | 0.6588479 | 0.0014608 | 0.5407395 | 0.8222253 |
| 9869 | SETDB1 | 0.7802729 | 0.0017989 | 0.5412213 | 0.8222253 |
| 84864 | MINA | 0.7142664 | 0.0015278 | 0.5451808 | 0.8222253 |
| 10735 | STAG2 | 0.8354065 | 0.0017597 | 0.5547007 | 0.8250203 |
| 1789 | DNMT3B | 0.4875240 | 0.0015198 | 0.5551428 | 0.8250203 |
| 3007 | HIST1H1D | 0.2165008 | 0.0016822 | 0.5603685 | 0.8292501 |
| 80205 | CHD9 | 0.7937180 | 0.0017674 | 0.5618366 | 0.8296612 |
| 26610 | ELP4 | 0.5447353 | 0.0016525 | 0.5737150 | 0.8340234 |
| 6598 | SMARCB1 | 0.0514494 | 0.0029348 | 0.5755599 | 0.8340234 |
| 4552 | MTRR | 0.7373405 | 0.0016159 | 0.5781484 | 0.8343052 |
| 64431 | ACTR6 | 0.7964734 | 0.0017459 | 0.5814011 | 0.8372656 |
| 57332 | CBX8 | 0.6620625 | 0.0018099 | 0.5885466 | 0.8403943 |
| 9274 | BCL7C | 0.6883955 | 0.0015587 | 0.5911020 | 0.8403943 |
| 29994 | BAZ2B | 0.2686543 | 0.0016847 | 0.5914767 | 0.8403943 |
| 6299 | SALL1 | 0.7896072 | 0.0016818 | 0.5919564 | 0.8403943 |
| 10036 | CHAF1A | 0.3012395 | 0.0022595 | 0.5956765 | 0.8412318 |
| 93973 | ACTR8 | 0.8599990 | 0.0017483 | 0.6047645 | 0.8413589 |
| 51616 | TAF9B | 0.4292715 | 0.0020349 | 0.6086993 | 0.8428907 |
| 8355 | HIST1H3G | 0.8769665 | 0.0017316 | 0.6092729 | 0.8428907 |
| 8349 | HIST2H2BE | 0.8808162 | 0.0018477 | 0.6161056 | 0.8453260 |
| 8971 | H1FX | 0.7975584 | 0.0017817 | 0.6207985 | 0.8500914 |
| 29072 | SETD2 | 0.8259135 | 0.0017726 | 0.6239638 | 0.8508431 |
| 8332 | HIST1H2AL | 0.8060010 | 0.0016974 | 0.6252378 | 0.8508431 |
| 6839 | SUV39H1 | 0.6644275 | 0.0017689 | 0.6262303 | 0.8508431 |
| 84733 | CBX2 | 0.1087613 | 0.0014613 | 0.6350208 | 0.8576195 |
| 79685 | SAP30L | 0.0623680 | 0.0024484 | 0.6397383 | 0.8576195 |
| 4591 | TRIM37 | 0.7989001 | 0.0018329 | 0.6434199 | 0.8576195 |
| 1911 | PHC1 | 0.5769332 | 0.0018927 | 0.6435223 | 0.8576195 |
| 138151 | NACC2 | 0.0128982 | 0.0027161 | 0.6464590 | 0.8598891 |
| 328 | APEX1 | 0.2881811 | 0.0018936 | 0.6521690 | 0.8617144 |
| 2186 | BPTF | 0.8288484 | 0.0017354 | 0.6534737 | 0.8617144 |
| 8290 | HIST3H3 | 0.6761244 | 0.0017682 | 0.6547854 | 0.8617144 |
| 1386 | ATF2 | 0.3682518 | 0.0015892 | 0.6574158 | 0.8617144 |
| 9275 | BCL7B | 0.8056415 | 0.0015979 | 0.6623813 | 0.8617144 |
| 55252 | ASXL2 | 0.4017567 | 0.0019069 | 0.6626670 | 0.8617144 |
| 6996 | TDG | 0.1863745 | 0.0018759 | 0.6716559 | 0.8641405 |
| 8350 | HIST1H3A | 0.6120455 | 0.0020072 | 0.6725535 | 0.8641405 |
| 10524 | KAT5 | 0.0360253 | 0.0017899 | 0.6749384 | 0.8641405 |
| 8473 | OGT | 0.4284415 | 0.0021886 | 0.6756909 | 0.8641405 |
| 8368 | HIST1H4L | 0.8811659 | 0.0017446 | 0.6830448 | 0.8661871 |
| 3018 | HIST1H2BB | 0.9192624 | 0.0018086 | 0.6901696 | 0.8714642 |
| 672 | BRCA1 | 0.0029921 | 0.0012163 | 0.6967982 | 0.8782430 |
| 10664 | CTCF | 0.8870007 | 0.0017337 | 0.7065975 | 0.8874723 |
| 8348 | HIST1H2BO | 0.7704641 | 0.0016555 | 0.7100036 | 0.8874723 |
| 29844 | TFPT | 0.7827575 | 0.0016687 | 0.7116461 | 0.8874723 |
| 5927 | KDM5A | 0.6751438 | 0.0021356 | 0.7263597 | 0.8992410 |
| 9759 | HDAC4 | 0.8810723 | 0.0018060 | 0.7382706 | 0.9097977 |
| 5928 | RBBP4 | 0.9446749 | 0.0018818 | 0.7388027 | 0.9097977 |
| 8365 | HIST1H4H | 0.9389097 | 0.0020161 | 0.7472166 | 0.9129609 |
| 6604 | SMARCD3 | 0.6477411 | 0.0017066 | 0.7492305 | 0.9129609 |
| 79828 | METTL8 | 0.7873235 | 0.0020193 | 0.7510440 | 0.9135736 |
| 56979 | PRDM9 | 0.0342685 | 0.0016262 | 0.7534212 | 0.9148687 |
| 55693 | KDM4D | 0.9478952 | 0.0018232 | 0.7586623 | 0.9180341 |
| 10734 | STAG3 | 0.0779382 | 0.0028245 | 0.7631101 | 0.9218158 |
| 200424 | TET3 | 0.5827257 | 0.0018635 | 0.7684779 | 0.9250934 |
| 55766 | H2AFJ | 0.8598732 | 0.0019617 | 0.7709295 | 0.9264446 |
| 7155 | TOP2B | 0.3757660 | 0.0019205 | 0.7736113 | 0.9280673 |
| 55506 | H2AFY2 | 0.8900352 | 0.0018245 | 0.7774429 | 0.9294644 |
| 55249 | YY1AP1 | 0.7884448 | 0.0018896 | 0.7835173 | 0.9315876 |
| 2073 | ERCC5 | 0.3469132 | 0.0018728 | 0.7873704 | 0.9315876 |
| 8467 | SMARCA5 | 0.7688751 | 0.0017718 | 0.7885748 | 0.9315876 |
| 3005 | H1F0 | 0.9665025 | 0.0018894 | 0.7945288 | 0.9327485 |
| 8336 | HIST1H2AM | 0.7180478 | 0.0015720 | 0.7984828 | 0.9327485 |
| 3008 | HIST1H1E | 0.5308329 | 0.0017009 | 0.7988982 | 0.9327485 |
| 2353 | FOS | 0.3718542 | 0.0015814 | 0.8049700 | 0.9351068 |
| 64754 | SMYD3 | 0.5165780 | 0.0022601 | 0.8072798 | 0.9357660 |
| 6045 | RNF2 | 0.2465449 | 0.0023677 | 0.8083934 | 0.9357660 |
| 8342 | HIST1H2BM | 0.9485984 | 0.0018824 | 0.8184152 | 0.9381969 |
| 55140 | ELP3 | 0.8461810 | 0.0018393 | 0.8203656 | 0.9381969 |
| 6883 | TAF12 | 0.9712324 | 0.0018479 | 0.8286729 | 0.9422267 |
| 8344 | HIST1H2BE | 0.8725188 | 0.0017585 | 0.8389631 | 0.9467150 |
| 79723 | SUV39H2 | 0.8480378 | 0.0020914 | 0.8528568 | 0.9526949 |
| 4255 | MGMT | 0.4225143 | 0.0017406 | 0.8550499 | 0.9526949 |
| 642636 | RAD21L1 | 0.8957358 | 0.0018693 | 0.8567153 | 0.9526949 |
| 3720 | JARID2 | 0.9734268 | 0.0019294 | 0.8672433 | 0.9594740 |
| 8335 | HIST1H2AB | 0.8566352 | 0.0019843 | 0.8712667 | 0.9623976 |
| 84444 | DOT1L | 0.9457172 | 0.0018499 | 0.8818866 | 0.9656724 |
| 3006 | HIST1H1C | 0.8244579 | 0.0016638 | 0.8836298 | 0.9656724 |
| 92815 | HIST3H2A | 0.8007033 | 0.0017142 | 0.8931993 | 0.9656724 |
| 80853 | KDM7A | 0.3186267 | 0.0015589 | 0.8947532 | 0.9656724 |
| 8607 | RUVBL1 | 0.7677550 | 0.0017436 | 0.8976321 | 0.9656724 |
| 8334 | HIST1H2AC | 0.9736561 | 0.0020215 | 0.9002402 | 0.9656724 |
| 3024 | HIST1H1A | 0.9919747 | 0.0019290 | 0.9021685 | 0.9659162 |
| 5929 | RBBP5 | 0.1157755 | 0.0018672 | 0.9042386 | 0.9659844 |
| 4798 | NFRKB | 0.3810459 | 0.0020732 | 0.9079597 | 0.9661800 |
| 23397 | NCAPH | 0.9520029 | 0.0018458 | 0.9160706 | 0.9705259 |
| 8345 | HIST1H2BH | 0.9913906 | 0.0019194 | 0.9165494 | 0.9705259 |
| 54107 | POLE3 | 0.4921221 | 0.0022789 | 0.9247095 | 0.9705259 |
| 1912 | PHC2 | 0.1336156 | 0.0018800 | 0.9250157 | 0.9705259 |
| 8367 | HIST1H4E | 0.6714368 | 0.0018814 | 0.9276948 | 0.9705259 |
| 23028 | KDM1A | 0.1678295 | 0.0023331 | 0.9357884 | 0.9764139 |
| 8340 | HIST1H2BL | 0.5714782 | 0.0017358 | 0.9465857 | 0.9824445 |
| 51317 | PHF21A | 0.9382791 | 0.0019681 | 0.9682743 | 0.9903361 |
| 9329 | GTF3C4 | 0.5973066 | 0.0016136 | 0.9689104 | 0.9903361 |
| 8968 | HIST1H3F | 0.4273824 | 0.0018692 | 0.9692350 | 0.9903361 |
| 3009 | HIST1H1B | 0.0815399 | 0.0036562 | 0.9841657 | 0.9966538 |
| 3607 | FOXK2 | 0.8184091 | 0.0021198 | 0.9963911 | 0.9992584 |
| 9219 | MTA2 | 0.7586908 | 0.0018994 | 0.9999977 | 0.9999977 |
[1] "Note, this is all 311 genes from the list using the pval.anthr column"# A tibble: 8 × 3
# Groups: id [4]
id time pvalue
<fct> <chr> <dbl>
1 Daunorubicin 24_hours 0.127
2 Daunorubicin 3_hours 0.00486
3 Doxorubicin 24_hours 0.137
4 Doxorubicin 3_hours 1.00
5 Epirubicin 24_hours 0.171
6 Epirubicin 3_hours 0.00853
7 Mitoxantrone 24_hours 0.0000543
8 Mitoxantrone 3_hours 1.00 Using Baysian gene set enrichment on Chromatin from Seoane
<environment: R_GlobalEnv>[1] 72
R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] readxl_1.4.2 broom_1.0.3 kableExtra_1.3.4 sjmisc_2.8.9
[5] scales_1.2.1 ggpubr_0.6.0 cowplot_1.1.1 RColorBrewer_1.1-3
[9] biomaRt_2.52.0 ggsignif_0.6.4 lubridate_1.9.2 forcats_1.0.0
[13] stringr_1.5.0 dplyr_1.1.0 purrr_1.0.1 readr_2.1.4
[17] tidyr_1.3.0 tibble_3.1.8 ggplot2_3.4.1 tidyverse_2.0.0
[21] limma_3.52.4 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] colorspace_2.1-0 ellipsis_0.3.2 sjlabelled_1.2.0
[4] rprojroot_2.0.3 XVector_0.36.0 fs_1.6.1
[7] rstudioapi_0.14 farver_2.1.1 bit64_4.0.5
[10] AnnotationDbi_1.58.0 fansi_1.0.4 xml2_1.3.3
[13] cachem_1.0.7 knitr_1.42 jsonlite_1.8.4
[16] dbplyr_2.3.1 png_0.1-8 compiler_4.2.2
[19] httr_1.4.5 backports_1.4.1 fastmap_1.1.1
[22] cli_3.6.0 later_1.3.0 htmltools_0.5.4
[25] prettyunits_1.1.1 tools_4.2.2 gtable_0.3.1
[28] glue_1.6.2 GenomeInfoDbData_1.2.8 rappdirs_0.3.3
[31] Rcpp_1.0.10 carData_3.0-5 Biobase_2.56.0
[34] cellranger_1.1.0 jquerylib_0.1.4 vctrs_0.5.2
[37] Biostrings_2.64.1 svglite_2.1.1 insight_0.19.0
[40] xfun_0.37 ps_1.7.2 rvest_1.0.3
[43] timechange_0.2.0 lifecycle_1.0.3 rstatix_0.7.2
[46] XML_3.99-0.13 getPass_0.2-2 zlibbioc_1.42.0
[49] vroom_1.6.1 hms_1.1.2 promises_1.2.0.1
[52] parallel_4.2.2 yaml_2.3.7 curl_5.0.0
[55] memoise_2.0.1 sass_0.4.5 stringi_1.7.12
[58] RSQLite_2.3.0 highr_0.10 S4Vectors_0.34.0
[61] BiocGenerics_0.42.0 filelock_1.0.2 GenomeInfoDb_1.32.4
[64] rlang_1.0.6 pkgconfig_2.0.3 systemfonts_1.0.4
[67] bitops_1.0-7 evaluate_0.20 labeling_0.4.2
[70] bit_4.0.5 processx_3.8.0 tidyselect_1.2.0
[73] magrittr_2.0.3 R6_2.5.1 IRanges_2.30.1
[76] generics_0.1.3 DBI_1.1.3 pillar_1.8.1
[79] whisker_0.4.1 withr_2.5.0 KEGGREST_1.36.3
[82] abind_1.4-5 RCurl_1.98-1.10 crayon_1.5.2
[85] car_3.1-1 utf8_1.2.3 BiocFileCache_2.4.0
[88] tzdb_0.3.0 rmarkdown_2.20 progress_1.2.2
[91] grid_4.2.2 blob_1.2.3 callr_3.7.3
[94] git2r_0.31.0 digest_0.6.31 webshot_0.5.4
[97] httpuv_1.6.9 stats4_4.2.2 munsell_0.5.0
[100] viridisLite_0.4.1 bslib_0.4.2