# 5.RNA Network

## 1) Table of Contents

在[CHIP-seq](/teaching/part-iii.-ngs-data-analyses/3.chip-seq.md)一节中，我们介绍了如何通过CHIP-seq数据分析确定特定转录因子和DNA的相互作用关系。本章中我们将介绍更多的推断生物大分子相互关系的生物信息学方法:

* [5.1.Co-expression Network](/teaching/part-iii.-ngs-data-analyses/5.rna-network/co_expression.md): 从表达矩阵出发，判断哪些基因有相似的表达模式
* [5.2.miRNA Targets](/teaching/part-iii.-ngs-data-analyses/5.rna-network/mirna-targets.md): 从序列出发，用生物信息学工具预测mirna的靶标
* [5.3.CLIP-seq (RNA-protein interactions)](/teaching/part-iii.-ngs-data-analyses/5.rna-network/clip-seq.md): 通过CLIP-seq数据分析确定特定RNA结合蛋白(RBP)和RNA的相互作用关系

## 2) Files Needed <a href="#files" id="files"></a>

### Method 1: Use docker

### 5.1 Co-expression Network

docker images的下载链接如[附表](/teaching/appendix/appendix-iv.-teaching.md#teaching-docker)所示，下载 bioinfo-coexp.tar.gz 启动新的docker.

```bash
# load image tarball
docker load -i ~/Downloads/bioinfo_coexp.tar.gz # 请根据下载文件的实际位置调整输入内容
docker run -dt --name coexpression --restart unless-stopped -v {host.machine.shared.directory}:/data gangxu/coexpression:1.5
docker exec -it coexpression bash
cd /home/bioc
```

### 5.2 miRNA target prediction

```bash
docker load -i ~/Downloads/bioinfo_mirna_target.tar.gz
docker run -dt --name mirna --restart unless-stopped -v {host.machine.shared.directory}:/data mirna_targets:1.0
docker exec -it mirna bash
cd /home/test/mirna
```

### 5.3 CLIP-seq data analysis

### Method 2: Directly Download

* 如果不使用docker，也可以直接从 [**Files needed** ](https://courses.ncrnalab.org/files)中的**Files/** 路径下的相应文件夹中下载所需要的文件。

## 3) Teaching Video

* see Videos in the [**Files needed** ](https://courses.ncrnalab.org/files)


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