植物GO注释

Posted 2020-11-13 zhanmaomao

本文主要是对没有GO term库的植物进行注释。

1、选用AgriGo 进行注释，在agriGO中点击species后，查看与你目标物种相近的物种作为库

 

 

 

2、比如我以甜菜为例

为了找到和GO term对应的ID，先找到PLAZA，进入网站https://bioinformatics.psb.ugent.be/plaza/versions/plaza_v3_dicots/download/index

点击data ->identifier Conversion, 找到甜菜，下载改ID对应的文件，进而可以确定甜菜基因组版本，并进行写脚本更换ID

3、将DGE更换好的ID输入AgriGO中，即可获得差异基因，可点击downlodw下载，

     选取FDR<=0.05, p <0.05进行作图

 

作图

使用ggplot2

rm(list = ls())

library(ggplot2)

 

data <- read.table("Go_input.txt",header = T,sep = " ")

attach(data)

dorder=factor(as.integer(row.names(data)),labels = data$Term)  ###sorted by the Term,

p <- ggplot(data,aes(x=dorder,y=queryitem,fill=term_type))+geom_bar(stat = "identity",width = 0.8)+

  xlab("") + ylab("Gene count") +theme_bw()+

  scale_fill_discrete(name="GO_category",breaks=c("C","F","P"),labels=c("CC","MF","BP"))+  ##change the legend text

  theme(panel.background = element_rect(fill = "transparent",colour = NA),axis.text.y = element_text(size = 7),axis.text.x = element_text(face = "bold",angle = 70,vjust = 1,hjust = 1,size = 7))