starbase(ENCORI)
数据库的简单介绍可以看下知乎这个视频
利用命令行工具curl批量下载miRNA预测的靶基因数据
ENCORI 界面点击Web API,出现API Panel包括八个应用:
1应用描述
2命令参数解释
3输出格式解释
4例子
API miRNA-Target
实际运用
首先需要文本文件
#miR.txt
hsa-miR-320c
hsa-miR-338-3p
hsa-miR-383-5p
hsa-miR-409-5p
hsa-miR-539-5p
hsa-miR-1238-3p
hsa-miR-545
hsa-let-7i*
hsa-miR-129*
hsa-miR-99a*
hsa-miR-3713
hsa-miR-4270
下载数据
我设置的参数为:
- clipExpNum='3'
- degraExpNum='1'
- pancancerNum='3'
- programNum='3'
- target='all'
#!/bin/bash
Bingin=`date +%s`
echo "$HOSTNAME"
echo "Doneload start now! "
echo
cat miR.txt |while read id;
do
CURL="curl 'http://starbase.sysu.edu.cn/api/miRNATarget/?assembly=hg19&geneType=mRNA&miRNA=${id}&clipExpNum=3&degraExpNum=1&pancancerNum=3&programNum=3&program=None&target=all&cellType=all'> ENCORI_hg19_CLIP-seq_${id}_all.txt"
echo -e "\n${id}\n${CURL}"
echo
echo
eval ${CURL}
done
End=`date +%s`
echo
echo "Doneload complete!"
Ttotal=`expr $End - $Bingin`
echo "Total time is: $Ttotal"
其中里面有几个miRNA 数据库里面没有检索到。
数据内容(选取了我认为重要的列):
miRNAname geneName chromosome clipExpNum clipExpNum degraExpNum RBP PITA RNA22 miRmap microT miRanda PicTar TargetScan pancancerNum
hsa-miR-383-5p MEAF6 chr1 8 8 1 AGO1-4,AGO2 1 0 1 0 1 0 0 3
hsa-miR-383-5p VPS72 chr1 7 7 0 AGO1-4,AGO2 1 0 1 0 1 0 0 5
hsa-miR-383-5p DDI2 chr1 4 4 0 AGO1-4,AGO2 1 0 0 1 1 0 1 3
hsa-miR-383-5p SFN chr1 7 7 2 AGO1-4,AGO2 1 0 0 0 1 1 0 9
hsa-miR-383-5p PRRX1 chr1 5 5 0 AGO1-4 1 0 1 0 1 0 0 3
hsa-miR-383-5p AP3M1 chr10 5 5 1 AGO1-4 1 0 1 0 1 0 0 3
hsa-miR-383-5p SHTN1 chr10 6 6 0 AGO1-4,AGO2 1 0 1 0 1 0 0 4
hsa-miR-383-5p PRDX3 chr10 18 18 2 AGO1,AGO1-4,AGO2 1 0 1 0 1 0 1 6
hsa-miR-383-5p DDX21 chr10 17 17 0 AGO1,AGO1-4,AGO2 1 0 1 1 1 0 0 5