Question: Target Network in Cytoscape
0
gravatar for adnanjaved1988
4.3 years ago by
Germany
adnanjaved198860 wrote:

Dear All

           I have xlsx file have miRNAs list  and Target genes.

hsa-miR-29a-3p
BCL7A; TNFAIP3; DICER1; CDK6; CDC42; BACE1; PXDN; PPP1R13B; DNMT3A; DNMT3B; COL4A1; COL4A2; MCL1; BCL2; CD276; DKK1; NAV3; SFRP2; ITIH5; S100B; IMPDH1; GLUL; PPM1D; PIK3R1; KREMEN2; FGG; FGA; FGB; LPL; CPEB3; CPEB4; ADAMTS9; ITGA11; NASP; NASP; PTEN; PTEN; ABL1; HBP1

 

 
hsa-miR-527, hsa-miR-518a-5p
      MCL1
hsa-miR-27a-3p
PAX3; IGF1; FOXO1; FBXW7; PHB; ZBTB10; MYT1; APC; THRB; SPRY2; WDR77; ABCA1; PDS5B; NFE2L2; EGFR

 

 
hsa-let-7b-5p
CDC34; RDH10; RPIA; ACTG1; HMGA2; CDC25A; CDK6; CCND1; CCND1; LIN28B; CCND2; NRAS; CCNA2; LIN28A; IFNB1; NR2E1; PRDM1; CYP2J2

 

 
hsa-miR-498
TERT; KRTAP5-9; RBFOX2

 Some miRNAs have more than one target genes and these target genes are separated by semicolon.If I use Cytoscape then those miRNAs which have more than one target genes they will be displaced by just one node and all those genes can not be seen separately they will be merged  but if I will have miRNAs in this shape for example  for last miRNAs

hsa-miR-498
hsa-let-7b-5p      TERT
hsa-let-7b-5p      KRTAP5-9
hsa-let-7b-5p      RBFOX2

If I will have miRNAs having more than one target genes in this format then individual gene can be displayed separately in   Cytoscape network..

Can you suggest me how I can make my xlsx file or txt file in this format in R??

 

rna-seq R gene • 1.4k views
ADD COMMENTlink modified 4.3 years ago by Jean-Karim Heriche18k • written 4.3 years ago by adnanjaved198860
0
gravatar for Jean-Karim Heriche
4.3 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche18k wrote:

It seems to me that you could easily convert your file into a format read by cytoscape like sif. Assuming that miRNAs are separated from targets by tabs then the following perl script should do it:

open FH,"<",$ARGV[0] or die "Failed to read file $ARGV[0]: $!";
while (my $line = <FH>) {
  next if ($line=~/^\s*$/); # Skip empty lines
  chomp($line);
  my ($miRNAs,$targets) = split(/\t+/,$line);
  my @miRNAs = split(/, /,$miRNAs);
  my @targets = split(/; /,$targets);
  foreach my $miRNA(@miRNAs) {
    foreach my $target(@targets) {
      print "$miRNA\t\t$target\n";
    }
  }
}
close FH;
ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Jean-Karim Heriche18k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 918 users visited in the last hour