Commit 4da916ae authored by Venkat Malladi's avatar Venkat Malladi

Analsyis of TCGA expression patterns.

parent 56b68b89
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# Filter for Bound vs unbound snoRNA that overlap with genes
## Filter for unbound snoRNA
bedtools intersect -a mcf-7-basal-snRNA_all.bed -b mcf-7-basal-snRNA_bound.bed -v > mcf-7-basal-snRNA_unbound.bed
# Intersect to find parent gene
bedtools intersect -wa -a gencode.v19.annotation_protein_coding.gtf -b mcf-7-basal-snRNA_bound.bed > mcf-7-basal-snRNA_bound_overlap.gtf
grep transcript mcf-7-basal-snRNA_bound_overlap.gtf | cut -f9 | cut -f1,2,5,8 -d ";" | cut -f2,4,6,8 -d " " | sed 's/"//g' | sed 's/;//g' | sort -u | sed 's/ /,/g' | grep ENST | sort | cut -f1 -d ',' | cut -f1 -d '.' | uniq > mcf-7-basal-snRNA_bound_overlap_host.txt
bedtools intersect -wa -a gencode.v19.annotation_protein_coding.gtf -b mcf-7-basal-snRNA_unbound.bed > mcf-7-basal-snRNA_unbound_overlap.gtf
grep transcript mcf-7-basal-snRNA_unbound_overlap.gtf | cut -f9 | cut -f1,2,5,8 -d ";" | cut -f2,4,6,8 -d " " | sed 's/"//g' | sed 's/;//g' | sort -u | sed 's/ /,/g' | grep ENST | sort | cut -f3 -d ',' | uniq > mcf-7-basal-snRNA_unbound_overlap_host.txt
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source("https://bioconductor.org/biocLite.R")
biocLite("SummarizedExperiment")
library(SummarizedExperiment)
load('/Users/venkatmalladi/TCGAbiolinksGUI/TCGA-BRCA_Gene_expression_Gene_expression_quantification_hg19.rda')
load('/Users/venkatmalladi/TCGAbiolinksGUI/TCGA-BRCA_clinical.rda')
# Analysis # Read in host gene
bound <- read.csv("./mcf-7-basal-snRNA_bound_overlap_host.txt", header=F, sep='\t')
bound$V1 <- as.character(bound$V1)
bound_gene_expression = data[rowRanges(data)$ensembl_gene_id %in% list(bound$V1)[[1]],]
unbound <- read.csv("./mcf-7-basal-snRNA_unbound_overlap_host.txt", header=F, sep='\t')
unbound$V1 <- as.character(unbound$V1)
unbound_gene_expression = data[rowRanges(data)$ensembl_gene_id %in% list(unbound$V1)[[1]],]
bound_rpkm <- unlist(data.frame(assays(bound_gene_expression)$normalized_count))
unbound_rpkm <- unlist(data.frame(assays(unbound_gene_expression)$normalized_count))
assays(bound_gene_expression)$normalized_count
jpeg('boxplot-bound_unbound.jpg')
boxplot(log2(unbound_rpkm+1),log2(bound_rpkm+1),col=(c("orange","blue")),yaxt="n", cex.axis=1,las=2,lwd=4,lty=1)
axis(2, at=seq(-10,25,5))
dev.off()
# Seperate into High ESR1,FOXA1, DRAIC
genes <- c("ENSG00000245750",'ENSG00000091831','ENSG00000129514')
expression_152 <- data[rowRanges(data)$ensembl_gene_id %in% genes,]
data_expression_152 <- t(data.frame(assays(expression_152)$normalized_count))
# Filter
data_expression_152_low_ESR1 <- data_expression_152[data_expression_152[,1] <= quantile(data_expression_152[1,],c(.10)),]
data_expression_152_high_ESR1 <- data_expression_152[data_expression_152[,1] > quantile(data_expression_152[1,],c(.10)),]
draic <- data.frame()
draic$low <- data_expression_152_low_ESR1[3]
jpeg('boxplot-DRAIC.jpg')
boxplot(log2(unlistdata_expression_152_low_ESR1[3]+1),log2(data_expression_152_high_ESR1[3]+1),col=(c("orange","blue")), cex.axis=1,las=2,lwd=4,lty=1)
dev.off()
TCGA-BRCA_clinical.rda
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