/
mechEindepQTL.Rmd
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mechEindepQTL.Rmd
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---
title: "Mechanism for each expression independent apaQTL"
author: "Briana Mittleman"
date: "2/3/2020"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
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.
```{r}
library(workflowr)
library(tidyverse)
```
```{r}
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)
```
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