Last updated: 2020-02-05

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Unstaged changes:
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    Deleted:    code/test.txt
    Deleted:    reads_graphs.Rmd

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

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 a1f5355 brimittleman 2020-02-05 add potential mechanisms and ld scripts
html cd33521 brimittleman 2020-02-05 Build site.
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 started
library(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-01

DIP2B: 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

longer isoform, decreased protein: * DIP2B

  • IF144L

  • RBBP5

  • STAP1

  • FAM207A

  • APOL2

  • EIF2A

  • STXB

longer isoform, increased protein:

  • C12orf72

  • OAS1

  • PSMF1

  • HTT

  • ERAP 1

  • SQSTM1

Intronic or coding PAS, decreased protein:

  • KPNB1

  • CCDC47

  • DOCK7

  • MGME1

  • PCYT1A

  • BTBD9

Intronic or coding PAS, increased protein:

  • NUP155

  • MPHOSPH10


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