PhyloP regulatory elements

Last updated: 2020-12-21

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Knit directory: Comparative_APA/analysis/

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Unstaged changes:
    Modified:   analysis/DeandNumPAS.Rmd
    Modified:   analysis/DirSelectionKhan.Rmd
    Modified:   analysis/ExploredAPA.Rmd
    Modified:   analysis/ExploredAPA_DF.Rmd
    Modified:   analysis/MMExpreiment.Rmd
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    Modified:   analysis/PTM_analysis.Rmd
    Modified:   analysis/ResultsNoUnlifted.Rmd
    Modified:   analysis/SetsdAPADIC.Rmd
    Modified:   analysis/TotalDomStructure.Rmd
    Modified:   analysis/TotalVNuclearBothSpecies.Rmd
    Modified:   analysis/annotationInfo.Rmd
    Modified:   analysis/changeMisprimcut.Rmd
    Modified:   analysis/comp2apaQTLPAS.Rmd
    Modified:   analysis/correlationPhenos.Rmd
    Modified:   analysis/dInforContent.Rmd
    Modified:   analysis/df_QC.Rmd
    Modified:   analysis/diffExpression.Rmd
    Modified:   analysis/establishCutoffs.Rmd
    Modified:   analysis/incorporateQTLsAncestral.Rmd
    Modified:   analysis/index.Rmd
    Modified:   analysis/infoContent.Rmd
    Modified:   analysis/investigatePantro5.Rmd
    Modified:   analysis/mRNADecay.Rmd
    Modified:   analysis/miRNAanalysis.Rmd
    Modified:   analysis/multiMap.Rmd
    Modified:   analysis/phastCon.Rmd
    Modified:   analysis/pol2.Rmd
    Modified:   analysis/speciesSpecific.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 repository in which changes were made to the R Markdown (analysis/phylopRegElements.Rmd) and HTML (docs/phylopRegElements.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
Rmd	d1e428d	brimittleman	2020-12-21	add intron and exon
html	0f74991	brimittleman	2020-12-21	Build site.
Rmd	2cfbc6d	brimittleman	2020-12-21	add phylop reg element analysis

library(workflowr)

This is workflowr version 1.6.2
Run ?workflowr for help getting started

library(cowplot)


********************************************************

Note: As of version 1.0.0, cowplot does not change the

  default ggplot2 theme anymore. To recover the previous

  behavior, execute:
  theme_set(theme_cowplot())

********************************************************

library(tidyverse)

── Attaching packages ────────────────────────────────── tidyverse 1.3.0 ──

✓ ggplot2 3.2.1     ✓ purrr   0.3.4
✓ tibble  2.1.3     ✓ dplyr   0.8.3
✓ tidyr   1.1.0     ✓ stringr 1.4.0
✓ readr   1.3.1     ✓ forcats 0.4.0

── Conflicts ───────────────────────────────────── tidyverse_conflicts() ──
x dplyr::filter() masks stats::filter()
x dplyr::lag()    masks stats::lag()

I will download regulatory elements and compare them to the PAS regions. I will run this for phylop20 and phlylop100

/project2/gilad/briana/Comparative_APA/data/RegElements

Download from table browser:

refseq elements
sno and miRNAs



python extractPhylopGeneral_20way.py   ../data/RegElements/hg38_RefSeqElements.bed ../data/RegElements/hg38_RefSeqElements.phyloP20.txt

python extractPhylopGeneral_20way.py  ../data/RegElements/hg38_snomiRNA.bed ../data/RegElements/hg38_snomiRNAphyloP20.txt 



python extractPhylopGeneral.py   ../data/RegElements/hg38_RefSeqElements.bed ../data/RegElements/hg38_RefSeqElements.phyloP100.txt

python extractPhylopGeneral.py  ../data/RegElements/hg38_snomiRNA.bed ../data/RegElements/hg38_snomiRNAphyloP100.txt

PAS_20=read.table("../data/PhyloP/PAS_Phylop20.txt", col.names = c("chr","start","end","PAS", "phyloP20"), stringsAsFactors = F) %>% drop_na() %>% mutate(element="PAS") %>% select(element,phyloP20)

PAS_100=read.table("../data/PhyloP/PAS_phyloP.txt", col.names = c("chr","start","end", "phyloP100"), stringsAsFactors = F) %>% drop_na()  %>%  mutate(element="PAS") %>% select(element,phyloP100)

Reg elements:

Reg_20= read.table("../data/RegElements/hg38_RefSeqElements.phyloP20.txt", col.names = c('chr', 'start', 'end', 'element', 'phyloP20' ), header = F, stringsAsFactors = F) %>% drop_na()%>% select(element, phyloP20)

RNAs_20=read.table("../data/RegElements/hg38_snomiRNAphyloP20.txt", col.names = c('chr', 'start', 'end', 'elementName', 'phyloP20' ), header = F, stringsAsFactors = F)%>% mutate(element="smallRNA") %>% drop_na()%>% select(element, phyloP20)

Reg_100= read.table("../data/RegElements/hg38_RefSeqElements.phyloP100.txt", col.names = c('chr', 'start', 'end', 'element', 'phyloP100' ), header = F, stringsAsFactors = F) %>% drop_na()%>% select(element, phyloP100)

RNAs_100=read.table("../data/RegElements/hg38_snomiRNAphyloP100.txt", col.names = c('chr', 'start', 'end', 'element_name', 'phyloP100' ), header = F, stringsAsFactors = F) %>% mutate(element="smallRNA") %>% drop_na() %>% select(element, phyloP100)

Look at the elements in the reg and decide which to include:

elementcount=Reg_20 %>% group_by(element) %>% summarise(nele=n()) %>% arrange(desc(nele))

regs_use=c("conserved_region", "enhancer", "CpG_island", "promoter", "silencer", "repeat_instability_region")

Will include: conserved_region, enhancer,CpG_island, promoter, silencer, repeat_instability_region

Reg_20_sm=Reg_20 %>% filter(element %in% regs_use)
Reg_100_sm=Reg_100 %>% filter(element %in% regs_use)


RegandRNA_20=Reg_20_sm %>% bind_rows(RNAs_20) %>% bind_rows(PAS_20) %>% mutate(fillcol=ifelse(element=="PAS", "yes", "no"))

RegandRNA_100=Reg_100_sm %>% bind_rows(RNAs_100) %>% bind_rows(PAS_100)%>% mutate(fillcol=ifelse(element=="PAS", "yes", "no"))

Plot:

phylop20plot=ggplot(RegandRNA_20, aes(x=element, y=phyloP20,fill=fillcol)) + geom_boxplot() + theme_classic() + labs(title="Regulatory element conservation", y="PhyloP 20 ways", x="")+ theme(axis.text.x = element_text(angle = 90), legend.position ="none")+ scale_fill_brewer(palette = "RdYlBu")
phylop20plot

Version	Author	Date
0f74991	brimittleman	2020-12-21

phylop100plot= ggplot(RegandRNA_100, aes(x=element, y=phyloP100,fill=fillcol)) + geom_boxplot() + theme_classic() + labs(title="Regulatory element conservation", y="PhyloP 100 ways", x="")+ theme(axis.text.x = element_text(angle = 90), legend.position ="none")+ scale_fill_brewer(palette = "RdYlBu")
phylop100plot

Version	Author	Date
0f74991	brimittleman	2020-12-21

both_together=plot_grid(phylop20plot,phylop100plot, nrow = 2)
both_together

Version	Author	Date
0f74991	brimittleman	2020-12-21

Add introns and exon:

get chr 1-22 from intron and exon file

subsetChr.py

main(fin, fout):
  small=open(fout, "w")
  chrkeep=["chr1", "chr2", 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21','chr22']
  for ln in open(fin,"r"):
    chrom=ln.split()[0]
    if chrom in chrkeep:
        small.write(ln)
  small.close()


if __name__ == "__main__":
    import sys
    infile = sys.argv[1]
    Outfile =sys.argv[2]
    main(infile, Outfile)

python subsetChr.py ../data/RegElements/hg38_ncbiRefseq_Formatted_Allannotation_noSNO.Resort.bed ../data/RegElements/hg38_ncbiRefseq_Formatted_Allannotation_noSNO.Resort.1.22.bed



python extractPhylopGeneral_20way.py  ../data/RegElements/hg38_ncbiRefseq_Formatted_Allannotation_noSNO.Resort.1.22.bed ../data/RegElements/phylop20_ncbi.txt

Allloc_20=read.table("../data/RegElements/phylop20_ncbi.txt", stringsAsFactors = F, header = F, col.names = c("chr", "start","end", "name", "phyloP20")) %>% separate(name, into=c("element", "gene"),sep=":") %>% drop_na() 

ggplot(Allloc_20, aes(x=element, y=phyloP20)) + geom_boxplot() + theme_classic()

Intron_20=Allloc_20 %>% filter(element=="intron") %>% select(element, phyloP20)

RegandRNAintron_20=Reg_20_sm %>% bind_rows(RNAs_20) %>% bind_rows(PAS_20) %>% bind_rows(Intron_20) %>%  mutate(fillcol=ifelse(element=="PAS", "yes", "no"))

ggplot(RegandRNAintron_20, aes(x=element, y=phyloP20,fill=fillcol)) + geom_boxplot() + theme_classic() + labs(title="Regulatory element conservation", y="PhyloP 20 ways", x="")+ theme(axis.text.x = element_text(angle = 90), legend.position ="none")+ scale_fill_brewer(palette = "RdYlBu")

promoter20= RegandRNAintron_20 %>% filter(element=="promoter")
enhan20= RegandRNAintron_20 %>% filter(element=="enhancer")
wilcox.test(PAS_20$phyloP20,Intron_20$phyloP20, alternative = "greater")


    Wilcoxon rank sum test with continuity correction

data:  PAS_20$phyloP20 and Intron_20$phyloP20
W = 5.0723e+10, p-value < 2.2e-16
alternative hypothesis: true location shift is greater than 0

wilcox.test(PAS_20$phyloP20,promoter20$phyloP20, alternative = "greater")


    Wilcoxon rank sum test with continuity correction

data:  PAS_20$phyloP20 and promoter20$phyloP20
W = 5925035, p-value = 0.00064
alternative hypothesis: true location shift is greater than 0

wilcox.test(PAS_20$phyloP20,enhan20$phyloP20, alternative = "greater")


    Wilcoxon rank sum test with continuity correction

data:  PAS_20$phyloP20 and enhan20$phyloP20
W = 26069436, p-value = 1
alternative hypothesis: true location shift is greater than 0

Allloc_100=read.table("../data/RegElements/phylop100_ncbi.txt", stringsAsFactors = F, header = F, col.names = c("chr", "start","end", "name", "phyloP100")) %>% separate(name, into=c("element", "gene"),sep=":") %>% drop_na()


Intron_100=Allloc_100 %>% filter(element=="intron") %>% select(element, phyloP100)

RegandRNAintron_100=Reg_100_sm %>% bind_rows(RNAs_100) %>% bind_rows(PAS_100) %>% bind_rows(Intron_100) %>%  mutate(fillcol=ifelse(element=="PAS", "yes", "no"))

ggplot(RegandRNAintron_100, aes(x=element, y=phyloP100,fill=fillcol)) + geom_boxplot() + theme_classic() + labs(title="Regulatory element conservation", y="PhyloP 100 ways", x="")+ theme(axis.text.x = element_text(angle = 90), legend.position ="none")+ scale_fill_brewer(palette = "RdYlBu")

promoter100= RegandRNAintron_100 %>% filter(element=="promoter")
enhan100= RegandRNAintron_100 %>% filter(element=="enhancer")
wilcox.test(PAS_100$phyloP100,Intron_100$phyloP100, alternative = "greater")


    Wilcoxon rank sum test with continuity correction

data:  PAS_100$phyloP100 and Intron_100$phyloP100
W = 4.7743e+10, p-value < 2.2e-16
alternative hypothesis: true location shift is greater than 0

wilcox.test(PAS_100$phyloP100,promoter100$phyloP100, alternative = "greater")


    Wilcoxon rank sum test with continuity correction

data:  PAS_100$phyloP100 and promoter100$phyloP100
W = 5533420, p-value = 0.01534
alternative hypothesis: true location shift is greater than 0

wilcox.test(PAS_100$phyloP100,enhan100$phyloP100, alternative = "greater")


    Wilcoxon rank sum test with continuity correction

data:  PAS_100$phyloP100 and enhan100$phyloP100
W = 22820110, p-value = 1
alternative hypothesis: true location shift is greater than 0

sessionInfo()

R version 3.6.1 (2019-07-05)
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_0.4.0   stringr_1.4.0   dplyr_0.8.3     purrr_0.3.4    
 [5] readr_1.3.1     tidyr_1.1.0     tibble_2.1.3    ggplot2_3.2.1  
 [9] tidyverse_1.3.0 cowplot_1.0.0   workflowr_1.6.2

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5         lubridate_1.7.4    lattice_0.20-38   
 [4] assertthat_0.2.1   rprojroot_1.3-2    digest_0.6.20     
 [7] R6_2.4.0           cellranger_1.1.0   backports_1.1.4   
[10] reprex_0.3.0       evaluate_0.14      httr_1.4.1        
[13] pillar_1.4.2       rlang_0.4.6        lazyeval_0.2.2    
[16] readxl_1.3.1       rstudioapi_0.10    whisker_0.3-2     
[19] Matrix_1.2-18      reticulate_1.16    rmarkdown_1.13    
[22] labeling_0.3       munsell_0.5.0      broom_0.5.2       
[25] compiler_3.6.1     httpuv_1.5.1       modelr_0.1.8      
[28] xfun_0.8           pkgconfig_2.0.2    htmltools_0.3.6   
[31] tidyselect_1.1.0   fansi_0.4.0        crayon_1.3.4      
[34] dbplyr_1.4.2       withr_2.1.2        later_0.8.0       
[37] grid_3.6.1         nlme_3.1-140       jsonlite_1.6      
[40] gtable_0.3.0       lifecycle_0.1.0    DBI_1.1.0         
[43] git2r_0.26.1       magrittr_1.5       scales_1.1.0      
[46] cli_2.2.0          stringi_1.4.3      farver_2.0.1      
[49] fs_1.3.1           promises_1.0.1     xml2_1.3.2        
[52] ellipsis_0.2.0.1   vctrs_0.3.0        generics_0.0.2    
[55] RColorBrewer_1.1-2 tools_3.6.1        glue_1.3.1        
[58] hms_0.5.3          yaml_2.2.0         colorspace_1.4-1  
[61] rvest_0.3.5        knitr_1.23         haven_2.3.1

PhyloP regulatory elements

Briana Mittleman

12/21/2020