复现1：AD的GWAS位点关联基因挖掘

作者: 小贝学生信 | 来源:发表于2021-05-10 17:03 被阅读0次

Title：Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration
PMID：31984958
Data/Code availability：Yes
IF：1.163
其它：paper来自JOVE的视频期刊，第一次了解，感觉挺有意思的
分析思路：如下，思路较为清晰明了，简单易行。首先根据其它文章里的AD GWAS数据找到关联基因(外显子、启动子、hiC的enhancer)，其中通过hiC的enhancer，寻找关联基因是本文的亮点所在。然后就是根据关联基因进行富集分析、不同AD分组差异表达分析、细胞类型差异表达分析。

paper思路
代码实操（R version 4.0.3 ）

0、安装包、下载数据

(1) 相关R包

BiocManager::install("GenomicRanges")
BiocManager::install("biomaRt")
BiocManager::install("WGCNA")
install.packages("reshape")
install.packages("ggplot2")
install.packages("corrplot")
install.packages("gProfileR")
install.packages("tidyverse")
install.packages("ggpubr")

（2）所有数据均可下载

1、credible SNPs for AD
https://static-content.springer.com/esm/art%3A10.1038%2Fs41588-018-0311-9/MediaObjects/41588_2018_311_MOESM3_ESM.xlsx
Before analysis, open sheet eight in 41588_2018_311_MOESM3_ESM.xlsx, remove the first three rows and save the sheet as Supplementary_Table_8_Jansen.txt with tab separated format.
2、10 kb resolution Hi-C interaction profiles in the adult brain from psychencode
http://adult.psychencode.org/Datasets/Integrative/Promoter-anchored_chromatin_loops.bed
3、exonic coordinates from Gencode version 19
https://www.jove.com/files/ftp_upload/60428/Gencode19_exon.bed
4、Promoters are defined as 2 kb upstream of transcription start site (TSS)
https://www.jove.com/files/ftp_upload/60428/Gencode19_promoter.bed
5、gene annotation from biomart
https://www.jove.com/files/ftp_upload/60428/geneAnno2.rda

1、制作GRanges对象（SNP、exon、promoter、HiC-enhancer）

GenomicRanges包的GRanges()函数创建

library(GenomicRanges) 
#SNP
credSNP = read.delim("Supplementary_Table_8_Jansen.txt", header=T,encoding = "UTF-8") 
#2357   19
credSNP = credSNP[credSNP$Credible.Causal=="Yes",]
#800    19
credranges = GRanges(credSNP$Chr, IRanges(credSNP$bp, credSNP$bp), rsid=credSNP$SNP, P=credSNP$P) 

#promoter and exonic region
exon = read.table("Gencode19_exon.bed")
exonranges = GRanges(exon[,1],IRanges(exon[,2],exon[,3]),gene=exon[,4])
promoter = read.table("Gencode19_promoter.bed")
promoterranges = GRanges(promoter[,1], IRanges(promoter[,2], promoter[,3]), gene=promoter[,4])

#HiC region
hic = read.table("Promoter-anchored_chromatin_loops.bed", skip=1)
colnames(hic) = c("chr", "TSS_start", "TSS_end", "Enhancer_start", "Enhancer_end")
hicranges = GRanges(hic$chr, IRanges(hic$TSS_start, hic$TSS_end), enhancer=hic$Enhancer_start)

2、寻找SNP与其它三种feature的Overlap

GenomicRanges包的findOverlaps()函数找overlap
findOverlaps(A, B)。其中A对应结果的queryHits，B对应结果的subjectHits

#（1）Overlap credible SNPs with exonic regions
olap = findOverlaps(credranges, exonranges)
credexon = credranges[queryHits(olap)]
#add gene info
mcols(credexon) = cbind(mcols(credexon), mcols(exonranges[subjectHits(olap)]))
#GRanges object with 42 ranges and 3 metadata columns:
#       seqnames    ranges strand |        rsid         P            gene
#          <Rle> <IRanges>  <Rle> | <character> <numeric>     <character>
#   [1]        1 161155392      * |   rs4575098  2.05e-10 ENSG00000158859
#   [2]        1 161156033      * |  rs11585858  5.58e-10 ENSG00000158859
#   [3]        1 207795320      * |   rs2296160  1.66e-17 ENSG00000203710


#（2）Overlap credible SNPs with promoter regions
olap = findOverlaps(credranges, promoterranges)
credpromoter = credranges[queryHits(olap)]
# add gene info
mcols(credpromoter) = cbind(mcols(credpromoter), 
mcols(promoterranges[subjectHits(olap)]))
#GRanges object with 236 ranges and 3 metadata columns:
#        seqnames    ranges strand |        rsid         P            gene
#           <Rle> <IRanges>  <Rle> | <character> <numeric>     <character>
#    [1]        2 234068476      * |  rs35349669  4.85e-09 ENSG00000168918
#    [2]        2 234068476      * |  rs35349669  4.85e-09 ENSG00000168918
#    [3]        2 234068705      * |  rs28669088  8.84e-09 ENSG00000168918

#（3）Overlap credible SNPs with hic-enhancer
## 先找hic interaction里与promoter存在overlap的loop
olap = findOverlaps(hicranges, promoterranges) 
hicpromoter = hicranges[queryHits(olap)]
mcols(hicpromoter) = cbind(mcols(hicpromoter), mcols(promoterranges[subjectHits(olap)]))
hicenhancer = GRanges(seqnames(hicpromoter), IRanges(hicpromoter$enhancer, hicpromoter$enhancer+10000), gene=hicpromoter$gene)
## 再基于上一步结果寻找与含promoter的hic的另一端"enhancer"存在重叠的variant
olap = findOverlaps(credranges, hicenhancer)
credhic = credranges[queryHits(olap)]
#add gene info
mcols(credhic) = cbind(mcols(credhic), mcols(hicenhancer[subjectHits(olap)]))

Integrate the 3 types GWAS targeted gene

ADgenes = Reduce(union, list(credhic$gene, credexon$gene, credpromoter$gene))
### to convert Ensembl Gene ID to HGNC symbol load("geneAnno.rda")
load("geneAnno2.rda")
ADhgnc = geneAnno1[match(ADgenes, geneAnno1$ensembl_gene_id), "hgnc_symbol"]
ADhgnc = ADhgnc[ADhgnc!=""]
save(ADgenes, ADhgnc, file="ADgenes.rda")
write.table(ADhgnc, file="ADgenes.txt", row.names=F, col.names=F, quote=F, sep="\t")

112 genes

library(reshape2)
library(ggplot2)
library(GenomicRanges)
library(biomaRt) 
library(WGCNA)

3、112个AD risk基因在Bulk RNA-seq的分组比较

#（1）整理表达矩阵
datExpr = read.csv("expression_matrix.csv", header = FALSE) 
datExpr = datExpr[,-1]  #17604  492
datMeta = read.csv("columns_metadata.csv") 
datProbes = read.csv("rows_metadata.csv")
datExpr = datExpr[datProbes$ensembl_gene_id!="",]   #17085  492
datProbes = datProbes[datProbes$ensembl_gene_id!="",]

#利用WGCGA包的collapseRows函数，针对重复基因的测序数据，取代表性的一个
datExpr.cr = collapseRows(datExpr, rowGroup = datProbes$ensembl_gene_id, rowID= rownames(datExpr))
class(datExpr.cr)
datExpr = datExpr.cr$datETcollapsed
gename = data.frame(datExpr.cr$group2row)
rownames(datExpr) = gename$group
#16279  492

# （2）分组信息
#Specify developmental stages
datMeta$Unit = "Postnatal"
idx = grep("pcw", datMeta$age) #postconceptional weeks
datMeta$Unit[idx] = "Prenatal" #产前

idx = grep("yrs", datMeta$age)
datMeta$Unit[idx] = "Postnatal" #产后
datMeta$Unit = factor(datMeta$Unit, levels=c("Prenatal", "Postnatal"))

# （3）选择大脑皮层区域的测序样本
datMeta$Region = "SubCTX"
r = c("A1C", "STC", "ITC", "TCx", "OFC", "DFC", "VFC", "MFC", "M1C", "S1C", "IPC", "M1C-S1C", "PCx", "V1C", "Ocx")
datMeta$Region[datMeta$structure_acronym %in% r] = "CTX"
datExpr = datExpr[,which(datMeta$Region=="CTX")]
#16279  345
datMeta = datMeta[which(datMeta$Region=="CTX"),]
#345  10

# （4）观察112个risk gene在两组的平均表达差异
load("ADgenes.rda")
#计算两组的均值（postnatal cortex与prenatal cortex）
exprdat = apply(datExpr[match(ADgenes, rownames(datExpr)),],2,mean,na.rm=T)
dat = data.frame(Region=datMeta$Region, Unit=datMeta$Unit, Expr=exprdat)

ggplot(dat,aes(x=Unit, y=Expr, fill=Unit, alpha=Unit)) + 
    geom_boxplot(outlier.size = NA) + 
    ggtitle("Brain Expression") + ylab("Normalized expression") + 
    xlab("") + scale_alpha_manual(values=c(0.2, 1)) + 
    theme_classic() + theme(legend.position="na")

4、观察112个risk gene在不同细胞类型的表达差异

#scRNA-seq 表达矩阵整理
cellexp = read.table("DER-20_Single_cell_expression_processed_TPM_backup.tsv",header=T,fill=T) 
cellexp[1121,1] = cellexp[1120,1] 
cellexp = cellexp[-1120,] 
rownames(cellexp) = cellexp[,1] 
cellexp = cellexp[,-1] 
datExpr = scale(cellexp,center=T, scale=F) 
datExpr = datExpr[,789:ncol(datExpr)] #15086    3461

#抽取112个gene的表达信息
targetname = "AD"
targetgene = ADhgnc
exprdat = apply(datExpr[match(targetgene, rownames(datExpr)),],2,mean,na.rm=T)
dat = data.frame(Group=targetname, cell=names(exprdat), Expr=exprdat)

#整理细胞类型
dat = dat[-grep("Ex|In",dat$celltype),] #不要神经元细胞
dat$celltype = gsub("Dev","Fetal",dat$celltype) #Dev替换为Fetal
dat$celltype = factor(dat$celltype, levels=c("Neurons","Astrocytes","Microglia","Endothelial", "Oligodendrocytes","OPC","Fetal"))

ggplot(dat,aes(x=celltype, y=Expr, fill=celltype)) +
    ylab("Normalized expression") + xlab("") + 
    geom_violin() + 
    theme(axis.text.x=element_text(angle = 90, hjust=1)) + 
    theme(legend.position="none") +
    ggtitle(paste0("Cellular expression profiles of AD risk genes"))
#AD risk genes are highly expressed in microglia

如下图结果展示，有多种多样的基因富集思路可供选择。

4、112个AD risk基因的富集分析（homer软件）

4.1 安装、下载、分析

#用conda安装
conda install -c bioconda homer
#下载背景data
perl /home/shensuo/miniconda3/envs/tmp/share/homer/.//configureHomer.pl -install
perl /home/shensuo/miniconda3/envs/tmp/share/homer/.//configureHomer.pl -install human-p 
perl /home/shensuo/miniconda3/envs/tmp/share/homer/.//configureHomer.pl -install human-o
#富集分析
findGO.pl ~/work/ADgenes.txt human ./go/ -cpu 5

富集分析结果

4.2 可视化

library(ggpubr)
plot_barplot = function(dbname,name,color){
    input = read.delim(paste0(dbname,".txt"),header=T) 
    input = input[,c(-1,-10,-11)] 
    input = unique(input)
    input$FDR = p.adjust(exp(input$logP)) 
    input_sig = input[input$FDR < 0.1,] 
    input_sig$FDR = -log10(input_sig$FDR) 
    input_sig = input_sig[order(input_sig$FDR),]
    p = ggbarplot(input_sig, x = "Term", y = "FDR", fill = color, 
        color = "white", sort.val = "asc", 
        ylab = expression(-log[10](italic(FDR))), xlab = paste0(name," Terms"), 
        rotate = TRUE, label = paste0(input_sig$Target.Genes.in.Term,"/",input_sig$Genes.in.Term), 
        font.label = list(color = "white", size = 9), lab.vjust = 0.5, lab.hjust = 1)
    p = p+geom_hline(yintercept = -log10(0.05), linetype = 2, color = "lightgray")
    return(p)
}
#以GO结果为例
plot_barplot("biological_process","GO Biological Process","#00AFBB")

GO enrichment

以上就是本篇paper全部的分析流程，的确很简单，对于我来说的收获有

1、GWAS的SNP与HiC的联合分析思路
2、Homer软件进行基因富集分析的强大之处（进一步学习）
3、WGCNA包里的collapseRows()函数处理重复基因测序的方法
4、GenomicRanges包找重叠区域的方法
.......

复现1：AD的GWAS位点关联基因挖掘

0、安装包、下载数据

(1) 相关R包

（2）所有数据均可下载

1、制作GRanges对象（SNP、exon、promoter、HiC-enhancer）

2、寻找SNP与其它三种feature的Overlap

3、112个AD risk基因在Bulk RNA-seq的分组比较

4、观察112个risk gene在不同细胞类型的表达差异

4、112个AD risk基因的富集分析（homer软件）

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