Last updated: 2020-05-05

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Knit directory: Comparative_APA/analysis/

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Unstaged changes:
    Modified:   analysis/DeandNumPAS.Rmd
    Modified:   analysis/ExploredAPA.Rmd
    Modified:   analysis/MMExpreiment.Rmd
    Modified:   analysis/OppositeMap.Rmd
    Modified:   analysis/PTM_analysis.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/establishCutoffs.Rmd
    Modified:   analysis/investigatePantro5.Rmd
    Modified:   analysis/mRNADecay.Rmd
    Modified:   analysis/multiMap.Rmd
    Modified:   analysis/pol2.Rmd
    Modified:   analysis/speciesSpecific.Rmd

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Rmd 850079c brimittleman 2020-05-05 add metrics during writing
html a7e29b9 brimittleman 2020-04-10 Build site.
Rmd 014951a brimittleman 2020-04-10 remove 18499
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Rmd 4e2a869 brimittleman 2020-03-19 add SS in opp
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Rmd 010c249 brimittleman 2020-01-21 DF species specific

In this analysis I want to look at the PAS that are identified at at least 10% in one species but are not identified in the other species. I will work with avergage nuclear. I can then run the differential apa analysis with only the PAS identified in both.

library(tidyverse)
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✔ 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()
library(ggpubr)
Loading required package: magrittr

Attaching package: 'magrittr'
The following object is masked from 'package:purrr':

    set_names
The following object is masked from 'package:tidyr':

    extract
PAS=read.table("../data/PAS_doubleFilter/PAS_5perc_either_HumanCoord_BothUsage_meta_doubleFilter.txt", header = T, stringsAsFactors = F)

HumanSpec= PAS %>% filter(Chimp==0)
nrow(HumanSpec)
[1] 302
ChimpSpec= PAS %>% filter(Human==0)
nrow(ChimpSpec)
[1] 357

This is a lot better. This is down from 2500 and 4000 respecively.

Look at the distribution of these accross the gene.

ggplot(HumanSpec,aes(x=loc,fill=loc)) + geom_bar(stat="count")  + labs(x="Genic location", y="Number of PAS", title="Location of Human Specific PAS") + scale_fill_brewer(palette = "Dark2")

Version Author Date
a7e29b9 brimittleman 2020-04-10
a7536f9 brimittleman 2020-04-03
332cbca brimittleman 2020-03-19
6c39a2a brimittleman 2020-01-21
ggplot(HumanSpec,aes(x=loc, y=Human, ,fill=loc)) + geom_boxplot()  + labs(x="Genic location", y="Human Average Usage", title="Human Specific PAS") + scale_fill_brewer(palette = "Dark2")

Version Author Date
a7e29b9 brimittleman 2020-04-10
a7536f9 brimittleman 2020-04-03
332cbca brimittleman 2020-03-19
6c39a2a brimittleman 2020-01-21
ggplot(ChimpSpec,aes(x=loc,fill=loc)) + geom_bar(stat="count")  + labs(x="Genic location", y="Number of PAS", title="Location of Chimp Specific PAS")+ scale_fill_brewer(palette = "Dark2")

Version Author Date
a7e29b9 brimittleman 2020-04-10
a7536f9 brimittleman 2020-04-03
332cbca brimittleman 2020-03-19
ggplot(ChimpSpec,aes(x=loc, y=Chimp, ,fill=loc)) + geom_boxplot()  + labs(x="Genic location", y="Chimp Average Usage", title="Chimp Specific PAS") + scale_fill_brewer(palette = "Dark2")

Version Author Date
a7e29b9 brimittleman 2020-04-10
a7536f9 brimittleman 2020-04-03
332cbca brimittleman 2020-03-19

Next I will see if these are due to low expression. I will pull in the average normalized expression and rerun the filter.

nameID=read.table("../../genome_anotation_data/ensemble_to_genename.txt",sep="\t", header = T, stringsAsFactors = F) %>% dplyr::select(Gene_stable_ID,Gene.name)
expr=read.table("../data/DiffExpression/NoramalizedExpression.txt",header = T,stringsAsFactors = F) %>% rename('Gene_stable_ID'=genes) %>% inner_join(nameID, by="Gene_stable_ID") %>% dplyr::select(Gene.name,Chimp, Human) %>% rename("ChimpExp"=Chimp, "HumanExp"=Human, "gene"=Gene.name)

PAS_exp=PAS %>% inner_join(expr,by="gene")
nrow(PAS_exp)
[1] 38771
nrow(PAS_exp)/nrow(PAS)
[1] 0.8725918
HumanSpecExp= PAS_exp %>% filter(Chimp==0)
nrow(HumanSpecExp)
[1] 231
nrow(HumanSpecExp)/nrow(HumanSpec)
[1] 0.7649007
ChimpSpecExp= PAS_exp %>% filter(Human==0)
nrow(ChimpSpecExp)
[1] 241
nrow(ChimpSpecExp)/nrow(ChimpSpec)
[1] 0.67507

We dont lose as many this way. This is evident the filter worked.

PAS_exp_spe=PAS_exp %>% mutate(HumanSpec=ifelse(gene %in%HumanSpecExp$gene, "yes", "no"), ChimpSpec=ifelse(gene %in% ChimpSpecExp$gene, "yes","no"))

ggplot(PAS_exp_spe,aes(x=HumanSpec,y=HumanExp)) + geom_boxplot() + stat_compare_means(method = "t.test") + labs(x="Presence of Human Specific PAS", y="Average Normalized Expression", title="Expression in Genes with Human Specific PAS")

Version Author Date
a7e29b9 brimittleman 2020-04-10
a7536f9 brimittleman 2020-04-03
332cbca brimittleman 2020-03-19
ggplot(PAS_exp_spe,aes(x=ChimpSpec,y=ChimpExp)) + geom_boxplot() + stat_compare_means(method = "t.test") + labs(x="Presence of Chimp Specific PAS", y="Average Normalized Expression", title="Expression in Genes with Chimp Specific PAS")

Version Author Date
a7e29b9 brimittleman 2020-04-10
a7536f9 brimittleman 2020-04-03
332cbca brimittleman 2020-03-19

Ask if signal sites account for this:

PASSS=read.table("../data/PAS_doubleFilter/PAS_5perc_either_HumanCoord_BothUsage_meta_doubleFilter_withSS.txt", header = T, stringsAsFactors = F) %>% dplyr::select(PAS,ChimpPAS ,HumanPAS)

HumanSpec_SS=HumanSpec %>% inner_join(PASSS, by="PAS")  %>% rename("HumanSS"= HumanPAS, "ChimpSS"=ChimpPAS) %>% mutate(OnlyHuman=ifelse(HumanSS!="None" & ChimpSS=="None", "Yes", "No"), OnlyChimp=ifelse(HumanSS=="None" & ChimpSS!="None", "Yes", "No"))
ChimpSpec_SS=ChimpSpec %>% inner_join(PASSS, by="PAS")%>% rename("HumanSS"= HumanPAS, "ChimpSS"=ChimpPAS) %>%  mutate(OnlyHuman=ifelse(HumanSS!="None" & ChimpSS=="None", "Yes", "No"),OnlyChimp=ifelse(HumanSS=="None" & ChimpSS!="None", "Yes", "No"))

Summary:

HumanSpec_SS$OnlyHuman= as.factor(HumanSpec_SS$OnlyHuman)

summary(HumanSpec_SS$OnlyHuman)
 No Yes 
294   8 
HumanSpec_SS$OnlyChimp= as.factor(HumanSpec_SS$OnlyChimp)

summary(HumanSpec_SS$OnlyChimp)
 No Yes 
299   3 
HumanSpec_SS %>% filter(OnlyHuman=="Yes") 
          PAS  disc         gene    loc   chr     start       end Chimp
1  human21341 Human       MSTO2P    end  chr1 155750935 155751135     0
2  human98439 Human       GPR180   utr3 chr13  94632911  94633111     0
3 human124552 Human     C15orf40   utr3 chr15  83004841  83005041     0
4 human154027 Human      L3MBTL4 intron chr18   6034146   6034346     0
5 human199184  Both        CFLAR intron  chr2 201125162 201125362     0
6 human254219 Human      SEPSECS   utr3  chr4  25120245  25120445     0
7 human288791 Human LOC102546294 intron  chr5 148282965 148283165     0
8 human359746 Human        NTRK2 intron  chr9  84768766  84768966     0
  Human strandFix ChimpSS HumanSS OnlyHuman OnlyChimp
1 0.154         +    None  AATATA       Yes        No
2 0.110         +    None  AATAAA       Yes        No
3 0.106         -    None  ATTAAA       Yes        No
4 0.050         -    None  ATTAAA       Yes        No
5 0.056         +    None  AATAAA       Yes        No
6 0.060         -    None  AATATA       Yes        No
7 0.066         -    None  AATAAA       Yes        No
8 0.050         +    None  GATAAA       Yes        No

Look at usage of these:

HumanSpec_SSexp=HumanSpec_SS  %>% filter(OnlyHuman=="Yes") 

ggplot(HumanSpec_SSexp,aes(x=loc, y=Human,fill=loc))+ geom_boxplot() + scale_fill_brewer(palette = "Dark2")

Version Author Date
a7e29b9 brimittleman 2020-04-10
a7536f9 brimittleman 2020-04-03
332cbca brimittleman 2020-03-19
ChimpSpec_SS$OnlyHuman= as.factor(ChimpSpec_SS$OnlyHuman)

summary(ChimpSpec_SS$OnlyHuman)
 No Yes 
352   5 
ChimpSpec_SS$OnlyChimp= as.factor(ChimpSpec_SS$OnlyChimp)

summary(ChimpSpec_SS$OnlyChimp)
 No Yes 
341  16 
ChimpSpec_SS %>% filter(OnlyChimp=="Yes")
           PAS  disc           gene    loc   chr     start       end
1   human32635 Human         GALNT2   utr3  chr1 230281327 230281527
2   chimp42565 Chimp     ENTPD1-AS1 intron chr10  95876254  95876449
3   chimp43312 Chimp         ENTPD7   utr3 chr10  99705169  99705369
4   chimp68589 Chimp   LOC105369771 intron chr12  52112354  52112554
5  chimp119363 Chimp         SMG1P2    end chr16  29542808  29543008
6  chimp127622 Chimp    MAP3K14-AS1 intron chr17  45261499  45261699
7  chimp128457 Chimp       LRRC37A2 intron chr17  46516506  46516706
8  chimp154263 Chimp         ZNF813 intron chr19  53479458  53479656
9  chimp206436 Chimp           EXOG    end  chr3  38526562  38526763
10 chimp208929 Chimp TMEM110-MUSTN1 intron  chr3  52889869  52890069
11 chimp214335 Chimp          LSAMP intron  chr3 116322842 116323042
12 chimp226080 Chimp         MAN2B2   utr3  chr4   6621293   6621496
13 chimp229702 Chimp       ABRAXAS1 intron  chr4  83480746  83480946
14 chimp281433 Chimp        PRKAR1B   utr5  chr7    727572    727772
15 chimp281737 Chimp          GNA12    end  chr7   2726153   2726352
16 chimp326468 Chimp         EXOSC2    end  chr9 130707299 130707501
        Chimp Human strandFix ChimpSS HumanSS OnlyHuman OnlyChimp
1  0.17916667     0         +  AAAAAA    None        No       Yes
2  0.06333333     0         -  AATAAA    None        No       Yes
3  0.12500000     0         +  AATAAA    None        No       Yes
4  0.05416667     0         -  CATAAA    None        No       Yes
5  0.57666667     0         -  AAAAAG    None        No       Yes
6  0.05333333     0         +  CATAAA    None        No       Yes
7  0.05500000     0         +  ATTAAA    None        No       Yes
8  0.08500000     0         +  TATAAA    None        No       Yes
9  0.14083333     0         +  AATAAA    None        No       Yes
10 0.06083333     0         -  ATTAAA    None        No       Yes
11 0.06916667     0         -  AATACA    None        No       Yes
12 0.27416667     0         +  AATAAA    None        No       Yes
13 0.15083333     0         -  ATTAAA    None        No       Yes
14 0.05833333     0         -  AAAAAG    None        No       Yes
15 0.14583333     0         -  AATAAA    None        No       Yes
16 0.05333333     0         +  AATACA    None        No       Yes

Look at usage of these:

ChimpSpec_SSexp=ChimpSpec_SS  %>% filter(OnlyChimp=="Yes") 

ggplot(ChimpSpec_SSexp,aes(x=loc, y=Chimp,fill=loc))+ geom_boxplot() + scale_fill_brewer(palette = "Dark2") + labs(title="Chimp location for Chimp specific PAS with added Signal",x="Genic Location", y="Chimp Mean Usage")

Version Author Date
a7e29b9 brimittleman 2020-04-10
a7536f9 brimittleman 2020-04-03
332cbca brimittleman 2020-03-19

About 5 percent in both.

interesting chimp specific in MAN2b2, there is an AATAAA

Number with opposite relationship.

 HumanSpec_SS  %>% filter(OnlyChimp=="Yes")
          PAS  disc  gene    loc   chr    start      end Chimp Human
1  human75472 Human CPNE8 intron chr12 38698410 38698610     0 0.064
2 human145886 Human LSM12    end chr17 44033553 44033753     0 0.062
3 human302070 Human RN7SK   utr5  chr6 52995520 52995720     0 0.056
  strandFix ChimpSS HumanSS OnlyHuman OnlyChimp
1         -  GATAAA    None        No       Yes
2         -  AAAAAA    None        No       Yes
3         +  GATAAA    None        No       Yes
ChimpSpec_SS %>% filter(OnlyHuman=="Yes")
          PAS  disc     gene  loc   chr    start      end      Chimp Human
1  chimp47145 Chimp     ANO9 utr3 chr11   420339   420538 0.05166667     0
2  chimp56104 Chimp    SPCS2 utr3 chr11 74976869 74977069 0.06750000     0
3 human101283  Both    OXA1L  cds chr14 22771186 22771386 0.05250000     0
4 chimp107271 Chimp     ADAL  cds chr15 43345803 43346003 0.06583333     0
5 chimp128483 Chimp LRRC37A2  end chr17 46550367 46550561 0.06083333     0
  strandFix ChimpSS HumanSS OnlyHuman OnlyChimp
1         -    None  AAAAAA       Yes        No
2         +    None  AATAAA       Yes        No
3         +    None  AAAAAG       Yes        No
4         +    None  ATTAAA       Yes        No
5         +    None  AAAAAG       Yes        No

location of PAS set

I will plot the location distributions of each of these after removing the species specific for the opposite species.

ChimpAll=PAS %>% filter(Chimp>0) %>% select(loc) %>% mutate(species="Chimp")

HumanAll=PAS %>% filter(Human>0) %>% select(loc) %>% mutate(species="Human")

BothAll=ChimpAll %>% bind_rows(HumanAll) %>% group_by(species,loc) %>% summarise(nLoc=n()) %>% ungroup() %>% group_by(species) %>% mutate(nSpecies=sum(nLoc),prop=nLoc/nSpecies) 

ggplot(BothAll,aes(x="",y=prop, fill=loc)) + geom_bar(stat="identity",width=1, color="white")+  coord_polar("y", start=0) +theme_void() + facet_grid(~species) + scale_fill_brewer(palette = "RdYlBu", name="Genic Location", labels=c("Coding", "5KB downstream", "Intronic","3' UTR", "5' UTR")) 

BothAll
# A tibble: 10 x 5
# Groups:   species [2]
   species loc     nLoc nSpecies   prop
   <chr>   <chr>  <int>    <int>  <dbl>
 1 Chimp   cds     7305    44130 0.166 
 2 Chimp   end     3799    44130 0.0861
 3 Chimp   intron 14095    44130 0.319 
 4 Chimp   utr3   17688    44130 0.401 
 5 Chimp   utr5    1243    44130 0.0282
 6 Human   cds     7308    44075 0.166 
 7 Human   end     3785    44075 0.0859
 8 Human   intron 14119    44075 0.320 
 9 Human   utr3   17620    44075 0.400 
10 Human   utr5    1243    44075 0.0282

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] ggpubr_0.2      magrittr_1.5    forcats_0.3.0   stringr_1.3.1  
 [5] dplyr_0.8.0.1   purrr_0.3.2     readr_1.3.1     tidyr_0.8.3    
 [9] tibble_2.1.1    ggplot2_3.1.1   tidyverse_1.2.1

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.5   reshape2_1.4.3     haven_1.1.2       
 [4] lattice_0.20-38    colorspace_1.3-2   generics_0.0.2    
 [7] htmltools_0.3.6    yaml_2.2.0         utf8_1.1.4        
[10] rlang_0.4.0        later_0.7.5        pillar_1.3.1      
[13] glue_1.3.0         withr_2.1.2        RColorBrewer_1.1-2
[16] modelr_0.1.2       readxl_1.1.0       plyr_1.8.4        
[19] munsell_0.5.0      gtable_0.2.0       workflowr_1.6.0   
[22] cellranger_1.1.0   rvest_0.3.2        evaluate_0.12     
[25] labeling_0.3       knitr_1.20         httpuv_1.4.5      
[28] fansi_0.4.0        broom_0.5.1        Rcpp_1.0.4.6      
[31] promises_1.0.1     scales_1.0.0       backports_1.1.2   
[34] jsonlite_1.6       fs_1.3.1           hms_0.4.2         
[37] digest_0.6.18      stringi_1.2.4      grid_3.5.1        
[40] rprojroot_1.3-2    cli_1.1.0          tools_3.5.1       
[43] lazyeval_0.2.1     crayon_1.3.4       whisker_0.3-2     
[46] pkgconfig_2.0.2    xml2_1.2.0         lubridate_1.7.4   
[49] assertthat_0.2.0   rmarkdown_1.10     httr_1.3.1        
[52] rstudioapi_0.10    R6_2.3.0           nlme_3.1-137      
[55] git2r_0.26.1       compiler_3.5.1