Comparisons with other data sets
ERM
2023-05-22
Last updated: 2023-05-22
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Knit directory: Cardiotoxicity/
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| File | Version | Author | Date | Message |
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| Rmd | de54fd5 | reneeisnowhere | 2023-05-22 | add Seoane data |
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’
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 |
Seaone 2019
Seone, Jose Chromatin gene comparison: comes from supp data NAT. MED 2019
ArrGWAS to 24 hour DEG genes p < 0.05
| 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 |
HFGWAS
| 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 |
CAD GWAS
| 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 |
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
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