starbase(ENCORI)
數(shù)據(jù)庫的簡(jiǎn)單介紹可以看下知乎這個(gè)視頻
利用命令行工具curl批量下載miRNA預(yù)測(cè)的靶基因數(shù)據(jù)
ENCORI 界面點(diǎn)擊Web API吼鱼，出現(xiàn)API Panel包括八個(gè)應(yīng)用：
1應(yīng)用描述
2命令參數(shù)解釋
3輸出格式解釋
4例子
API miRNA-Target
實(shí)際運(yùn)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
下載數(shù)據(jù)
我設(shè)置的參數(shù)為：
- 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"
其中里面有幾個(gè)miRNA 數(shù)據(jù)庫里面沒有檢索到镊绪。
數(shù)據(jù)內(nèi)容(選取了我認(rèn)為重要的列)：
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
