> For the complete documentation index, see [llms.txt](https://zpliu.gitbook.io/booknote/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://zpliu.gitbook.io/booknote/ke-bian-jian-qie/shu-ju-chu-li-liu-cheng/20200102go-fu-ji-fen-xi.md).

# 20200102GO富集分析

对分好类的基因对进行GO功能富集分析

## 第一类conserve pattern

### 1.在各个基因组都存在相同的IR

> <http://bioinfo.cau.edu.cn/agriGO/analysis_precheck.php?session=863404143>

```bash
awk -F "_" '{print $1"_"$2}' ../converse/1_1 |sort|uniq|xargs  -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold |awk '{print $1"\n"$3}' |xargs -I {} grep {} ~/genome_data/Ghirsutum_genome_HAU_v1.1/Gh_Noscagenes_GO_V3.annot >1_1.go
```

### 2.在各个基因组中都不存在IR的基因对

> <http://bioinfo.cau.edu.cn/agriGO/analysis_precheck.php?session=913752380>

```bash
awk '{print $1"\n"$3}' ../converse/1_2|sort|uniq|xargs  -I {} grep {} ~/genome_data/Ghirsutum_genome_HAU_v1.1/Gh_Noscagenes_GO_V3.annot  >1_2.go
```

### 3.在A基因组中存在保守的IR

> <http://bioinfo.cau.edu.cn/agriGO/analysis_precheck.php?session=596719406>

```bash
awk -F "_" '{print $1}' ../converse/1_3 |sort|uniq|xargs  -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold |awk '{print $1"\n"$3}' |xargs -I {} grep {} ~/genome_data/Ghirsutum_genome_HAU_v1.1/Gh_Noscagenes_GO_V3.annot  >1_3.go
```

### 4.在D基因组中存在保守的IR

> <http://bioinfo.cau.edu.cn/agriGO/analysis_precheck.php?session=642301472>

```bash
awk -F "_" '{print $1"_"$2}' ../converse/1_4 |sort|uniq|xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold | awk '{print $1"\n"$3}' | xargs -I {} grep {} ~/genome_data/Ghirsutum_genome_HAU_v1.1/Gh_Noscagenes_GO_V3.annot >1_4.go
```

## 第二类IR在多倍化中发生丢失

### 1.只在Dt中发生IR丢失

> <http://bioinfo.cau.edu.cn/agriGO/analysis_precheck.php?session=819544063>

```bash
awk -F "_" '{print $1"_"$2}' ../converse/2_1 | sort | uniq | xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold | awk '{print $1"\n"$3}' | xargs -I {} grep {} ~/genome_data/Ghirsutum_genome_HAU_v1.1/Gh_Noscagenes_GO_V3.annot > 2_1.go
```

### 2.只在At中发生IR丢失

> <http://bioinfo.cau.edu.cn/agriGO/analysis_precheck.php?session=472631356>

```bash
awk -F "_" '{print $1"_"$2}' ../converse/2_2 | sort | uniq | xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold | awk '{print $1"\n"$3}' | xargs -I {} grep {} ~/genome_data/Ghirsutum_genome_HAU_v1.1/Gh_Noscagenes_GO_V3.annot > 2_2.go
```

### 3.在两个基因组中都发生了丢失

> <http://bioinfo.cau.edu.cn/agriGO/analysis_precheck.php?session=415512684>

```bash
## 将第四类的情况也统计到这里
 awk -F "_" '{print $1}' ../converse/2_3|sort | uniq | xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold | awk '{print $1"\n"$3}' | xargs -I {} grep {} ~/genome_data/Ghirsutum_genome_HAU_v1.1/Gh_Noscagenes_GO_V3.annot >2_3.go

## 只在A2中发生IR的事件
cut -f5 ../converseBed/A2.bed | awk -F "_" '{print $1}'|sort | uniq | xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold | awk '{print $1"\n"$3}' | xargs -I {} grep {} ~/genome_data/Ghirsutum_genome_HAU_v1.1/Gh_Noscagenes_GO_V3.annot >>2_3.go
## 只在D5中发生的IR事件
cut -f5 ../converseBed/D5.bed |awk -F "_" '{print $1}'|sort | uniq | xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold | awk '{print $1"\n"$3}' | xargs -I {} grep {} ~/genome_data/Ghirsutum_genome_HAU_v1.1/Gh_Noscagenes_GO_V3.annot >>2_3.go

sort 2_3.go |uniq >1 
mv 1 2_3.go
```

## 第三类IR在多倍化中获得新的IR事件

### 1.只在At中发生IR获得

> <http://bioinfo.cau.edu.cn/agriGO/analysis_precheck.php?session=893002877>

```bash
cut -f5 ../converseBed/At.bed |awk -F "_" '{print $1"_"$2}' |sort | uniq | xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold | awk '{print $1"\n"$3}' | xargs -I {} grep {} ~/genome_data/Ghirsutum_genome_HAU_v1.1/Gh_Noscagenes_GO_V3.annot >3_1.go
```

### 2.只在Dt中发生IR获得

> <http://bioinfo.cau.edu.cn/agriGO/analysis_precheck.php?session=566100874>

```bash
cut -f5 ../converseBed/Dt.bed |awk -F "_" '{print $1"_"$2}' |sort | uniq | xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold | awk '{print $1"\n"$3}' | xargs -I {} grep {} ~/genome_data/Ghirsutum_genome_HAU_v1.1/Gh_Noscagenes_GO_V3.annot >3_3.go
```

### 3.在两个基因组中都发生了获得

> <http://bioinfo.cau.edu.cn/agriGO/analysis_precheck.php?session=205614710>

这里包括第四类中的前两类

```bash
cat ../converse/3_2  ../converse/4_1  ../converse/4_2 |awk -F "_" '{print $1"_"$2}'|xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold | awk '{print $1"\n"$3}'|sort |uniq |xargs -I {} grep {} ~/genome_data/Ghirsutum_genome_HAU_v1.1/Gh_Noscagenes_GO_V3.annot >3_2.go
```

## 查看不同类别之间共有的GO号

先对文件进行筛选

```bash
##根据FDR<=0.05 筛选GO结果
awk -F "\t" '$8<=0.01&&$9<=0.01{print $1,$2,$3,$8,$9}' OFS="\t"
```

#### partition splicing pattern

二倍体直系同源基因都存在多种剪切模式，在多倍化之后，分别只继承在单个亚基因组中，说明可变剪切在亚基因组上发生了partition

```bash
## 提取对应的基因
grep GO:0010027 raw/2_1.txt |awk -F "\t" '{print $10}'|sed -e 's/\/\//\n/g' -e 's/ //g'
```

## 2020-01-07

讨论多倍化过程中AS的变化

### 两个亚基因组出现同样AS

#### 同时存在AS

* 1\_1&#x20;
* 3\_2
* 4\_1
* 4\_2

```bash
awk -F "_" '{print $1"_"$2}' ../converse/1_1 |sort|uniq|xargs  -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold >geneid/1_1.txt

cat ../converse/3_2  ../converse/4_1  ../converse/4_2 |awk -F "_" '{print $1"_"$2}'|xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold |sort|uniq >geneid/3_2.txt 

 awk -F "_" '{print $1"_"$2}' ../converse/4_1 |sort|uniq|xargs  -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold >geneid/4_1.txt

 awk -F "_" '{print $1"_"$2}' ../converse/4_2 |sort|uniq|xargs  -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold >geneid/4_2.txt
```

#### 同时不存在AS

四个基因组都不存在AS的基因对先不分析

* 2\_3
* 4\_3
* 4\_4

```bash
 awk -F "_" '{print $1}' ../converse/2_3|sort | uniq | xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold  >geneid/2_3.txt

 awk -F "_" '{print $1}' ../converse/4_3 |sort | uniq | xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold  >geneid/4_3.txt

  awk -F "_" '{print $1}' ../converse/4_4 |sort | uniq | xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold  >geneid/4_4.txt
```

### 两个亚基因组有不同的AS

#### 只在At中存在

* 1\_3
* 2\_1
* 3\_1
* 5\_2

```bash
  awk -F "_" '{print $1}' ../converse/1_3 |sort | uniq | xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold  >geneid/1_3.txt

  awk -F "_" '{print $1"_"$2}' ../converse/2_1 |sort | uniq | xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold  >geneid/2_1.txt

   awk -F "_" '{print $1"_"$2}'  ../converse/3_1 |sort | uniq | xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold  >geneid/3_1.txt

     awk -F "_" '{print $1"_"$2}'  ../converse/5_2 |sort | uniq | xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold  >geneid/5_2.txt
```

#### 只在Dt中存在

* 1\_4
* 2\_2
* 3\_3
* 5\_1

```bash
awk -F "_" '{print $1"_"$2}' ../converse/1_4 |sort | uniq | xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold  >geneid/1_4.txt

awk -F "_" '{print $1"_"$2}' ../converse/2_2 |sort | uniq | xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold  >geneid/2_2.txt

awk -F "_" '{print $1"_"$2}' ../converse/3_3 |sort | uniq | xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold  >geneid/3_3.txt

awk -F "_" '{print $1"_"$2}' ../converse/5_1 |sort | uniq | xargs -I {} grep {} ../../../../GhDt_Gr_GhAt_Ga_end_noScaffold  >geneid/5_1.txt
```

### 分别进行GO富集分析

在At中有的可变剪切，而Dt中没有可变剪切；