对miRNAs靶基因进行批量预测

1.提取miRNAs

cat mirna.txt
hsa-miR-378b
hsa-miR-4295
hsa-miR-325
hsa-miR-1286
hsa-miR-346

2. 由starbase API数据库进行下载(10s检索完成）

time cat mirna.txt |while read id;do echo $id;\
curl http://starbase.sysu.edu.cn/api/miRNATarget/?assembly=hg19\&geneType=mRNA\&miRNA=${id}\&clipExpNum=0\&degraExpNum=0\&pancancerNum=0\&programNum=1\&program=None\&target=all\&cellType=all > mirna/$id.txt;
done
real    0m7.955s
user    0m0.044s
sys     0m0.062s

3.将所有的miRNA靶基因进行合并整理

每个文件都有这么一个类似的表头，与lncRNA分析的那篇文章类似

#please cite:
#1.Zhou KR, Liu S, Cai L, Bin L, et al. ENCORI: The Encyclopedia of RNA Interactomes.
#2.Li JH, et al.starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data , Nucleic Acids Res. 2014 Jan;42:D92-7.
miRNAid miRNAname       geneID  geneName        geneType        chromosome      start   end     strand  clipExpNum      degraExpNum     RBP     merClass   miRseq  align   targetSeq       pancancerNum
The "target" parameter haven't been set correctly! Or the input of "target" parameter is not available!

合并所有的txt文件，并提取靶基因信息

cat *.txt > merge.txt
#删除注释行，删除行头，删除没有target的报错信息，
#最后获取第2例miRNA，第4例lncRNA
cat merge.txt |grep -v "#"|grep -v "chromosome"|grep -v "target"|cut -f2,4|less -SN
     1 hsa-miR-1286    VAMP7
      2 hsa-miR-1286    UBE2J2
      3 hsa-miR-1286    UBE2J2
      4 hsa-miR-1286    DVL1
      5 hsa-miR-1286    DVL1
      6 hsa-miR-1286    CCNL2
      7 hsa-miR-1286    CCNL2
      8 hsa-miR-1286    NADK
      9 hsa-miR-1286    NADK
     10 hsa-miR-1286    MMEL1
     11 hsa-miR-1286    CHD5
     12 hsa-miR-1286    ICMT
     13 hsa-miR-1286    ICMT
     14 hsa-miR-1286    ICMT
     15 hsa-miR-1286    ACOT7