Last updated: 2020-02-04
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Knit directory: apaQTL/analysis/
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These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 9062348 | brimittleman | 2020-02-05 | add some info about each gene |
In this analysis I will pull in the apaQTLs that are pQTLs or riboQTLs but are not eQTLs. I will look at their UTRs to think about mechanisms.
library(workflowr)This is workflowr version 1.5.0
Run ?workflowr for help getting startedlibrary(tidyverse)── Attaching packages ─────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──✔ ggplot2 3.1.1 ✔ purrr 0.3.2
✔ tibble 2.1.1 ✔ dplyr 0.8.0.1
✔ tidyr 0.8.3 ✔ stringr 1.3.1
✔ readr 1.3.1 ✔ forcats 0.3.0 ── Conflicts ────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()QTLs=read.table("../data/ExpressionIndependentapaQTLs.txt",header = T,stringsAsFactors = F)
QTLs %>% select(Gene, PAS_ID, apa_EffectSize,protein_EffectSize,protein_pvalue,ribo_EffectSize,ribo_pvalue) Gene PAS_ID apa_EffectSize protein_EffectSize protein_pvalue
1 DIP2B peak29441 1.692200 0.577281 3.75077e-02
2 C12orf73 peak32115 -1.108700 -0.326038 2.71335e-02
3 OAS1 peak32770 1.318360 -0.346212 1.14975e-02
4 OAS1 peak32773 -0.929530 -0.346212 1.14975e-02
5 KPNB1 peak57020 1.421620 -0.395942 2.76502e-02
6 CCDC47 peak58097 -2.256670 -0.741908 2.84767e-02
7 DOCK7 peak4419 1.049750 -0.388189 1.03583e-03
8 IFI44L peak4983 -1.238370 0.818405 2.77868e-03
9 STXBP3 peak6151 -1.538770 -0.316660 3.51995e-02
10 RBBP5 peak11391 0.923930 -0.380608 1.51308e-02
11 PSMF1 peak79280 2.001150 -0.531405 2.49467e-02
12 MGME1 peak79876 -1.753830 -0.652345 8.12206e-03
13 FAM207A peak83657 -0.799235 -0.494910 8.66305e-03
14 FAM207A peak83658 0.734096 -0.494910 8.66305e-03
15 APOL2 peak85064 0.875972 -0.872609 5.61694e-09
16 APOL2 peak85065 -0.758514 -0.825074 7.56307e-08
17 MPHOSPH10 peak71209 1.153580 0.423751 1.85688e-02
18 SACM1L peak88511 -0.852296 0.721947 5.51729e-05
19 EIF2A peak93068 -1.192200 0.443817 6.63713e-06
20 EIF2A peak93069 1.156360 0.443817 6.63713e-06
21 EIF2A peak93071 -0.951787 0.443817 6.63713e-06
22 PCYT1A peak94996 0.719192 -0.413925 4.01890e-02
23 HTT peak95775 0.607002 -0.234823 6.86209e-03
24 STAP1 peak97824 -0.476586 -0.310470 4.15434e-02
25 STAP1 peak97825 0.521675 -0.310470 4.15434e-02
26 NUP155 peak102907 1.405490 0.317654 2.73588e-02
27 ERAP1 peak105869 -2.295990 -0.610165 2.13488e-02
28 SQSTM1 peak110046 -1.516840 -0.500478 4.38725e-02
29 BTBD9 peak113151 1.558610 -0.396262 1.20583e-03
30 STX17 peak135747 0.862076 -0.353277 2.40948e-02
ribo_EffectSize ribo_pvalue
1 0.17633900 4.06124e-01
2 -0.28049400 1.07945e-01
3 -0.33146500 9.74889e-03
4 -0.33146500 9.74889e-03
5 0.14953000 6.62853e-02
6 0.29630300 2.09774e-01
7 -0.08647700 4.23490e-01
8 0.75124700 1.82275e-02
9 -0.01052120 9.42093e-01
10 -0.02045960 8.18195e-01
11 -0.24711400 1.52763e-01
12 -0.20593100 2.92921e-01
13 -0.11527400 4.93858e-01
14 -0.11527400 4.93858e-01
15 -0.33475400 8.33273e-02
16 -0.35391800 6.61021e-02
17 0.09587500 4.95768e-01
18 0.73145500 8.10980e-07
19 0.32571900 4.45356e-03
20 0.32571900 4.45356e-03
21 0.32571900 4.45356e-03
22 -0.17136000 1.89583e-01
23 -0.07689020 3.77708e-01
24 -0.03932920 8.22068e-01
25 -0.03932920 8.22068e-01
26 -0.10594500 4.20130e-01
27 -0.46341200 1.58962e-02
28 -0.27186100 2.68988e-01
29 -0.00511165 9.81933e-01
30 -0.11446700 4.64598e-01DIP2B: QTL in proximal UTR, hsa-miR-143-3p, hsa-miR-6088, hsa-miR-4770, miRNAs are upstream of first
The K box (cTGTGATa) is present in one or more copies in many of these 3’UTRs and mediates negative post-transcriptional regulation, mainly effected by decreased transcript levels.
C12orf73: 2nd of 3 UTR PAS: - POLR2A binding sites -hsa-miR-9-5p
OAS1:
IFI44L: between 2 UTR FOS binding site
STXBP3: PUM1 binding in 3’ UTR, translational regulator of specific mRNAs by binding to their 3’ untranslated regions, reported kbox, many miRNAs conserved (miR-15-5p/16-5p/195-5p/424-5p/497-5p)
RBBP5: extended isoform,reported Brd-Box (Brd) The Brd box (AGCTTTA) is present in one or more copies in many of these 3’UTRs and mediates negative post-transcriptional regulation by affecting transcript stability and translational efficiency. hsa-miR-338-3p
PSMF1: UNR binding site: In humans, UNR has been implicated in the destabilization of c-fos mRNA (Chang et al., 2004) and the activation of translation driven by the IRESs of a number of transcripts, including c-myc, miR-103-3p/107
MGME1- RBP binding for AQR, NIPBL, FUS (no DB results)
FAM207A- (no DB results)
APOL2- reported UNR binding site, SAFB binding between PAS in UTR
MPHOSPH10-
SACM1L-miR-181-5p
EIF2A- annotated Brd-Box (Brd) site between middle 2 utr binding sites, reported kbox as well
PCYT1A- (no DB results) many binding sites between annotated utr and end PAS, miR-142-3p.2
HTT: BRD-BOX, hsa-miR-216b-5p
STAP1- LTR/ERVL-MaLR repete element
NUP155-KBOX, BRD BOX , GLUT1 element, miR-199-3p, hsa-miR-3129-5p
ERAP1-MBE element - related to temporal regulation ,hsa-miR-4770, hsa-miR-143-3p, hsa-miR-6088
SQSTM1- FLAM_A - SINE/Alu repeate, GY-BOX- involved in RNA duplexes, hsa-miR-7-5p
BTBD9- GY-BOX, conserved hsa-miR-212-5p binding site , hsa-miR-212-5p
STX17- GY-BOX, BRD BOX, k-box, miR-15-5p/16-5p/195-5p/424-5p/497-5p
Lit search for BRD box and K box only has results for human, info about regulation in drosophila
sessionInfo()R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] forcats_0.3.0 stringr_1.3.1 dplyr_0.8.0.1 purrr_0.3.2
[5] readr_1.3.1 tidyr_0.8.3 tibble_2.1.1 ggplot2_3.1.1
[9] tidyverse_1.2.1 workflowr_1.5.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.2 cellranger_1.1.0 plyr_1.8.4 compiler_3.5.1
[5] pillar_1.3.1 later_0.7.5 git2r_0.26.1 tools_3.5.1
[9] digest_0.6.18 lubridate_1.7.4 jsonlite_1.6 evaluate_0.12
[13] nlme_3.1-137 gtable_0.2.0 lattice_0.20-38 pkgconfig_2.0.2
[17] rlang_0.4.0 cli_1.1.0 rstudioapi_0.10 yaml_2.2.0
[21] haven_1.1.2 withr_2.1.2 xml2_1.2.0 httr_1.3.1
[25] knitr_1.20 hms_0.4.2 generics_0.0.2 fs_1.3.1
[29] rprojroot_1.3-2 grid_3.5.1 tidyselect_0.2.5 glue_1.3.0
[33] R6_2.3.0 readxl_1.1.0 rmarkdown_1.10 modelr_0.1.2
[37] magrittr_1.5 whisker_0.3-2 backports_1.1.2 scales_1.0.0
[41] promises_1.0.1 htmltools_0.3.6 rvest_0.3.2 assertthat_0.2.0
[45] colorspace_1.3-2 httpuv_1.4.5 stringi_1.2.4 lazyeval_0.2.1
[49] munsell_0.5.0 broom_0.5.1 crayon_1.3.4