File#1:

GeneID  ColA    ColB
Gene01  5   15
Gene02  4   8
Gene03  25  5

File#2:

GeneID  ColA    ColC
Gene01  12  3
Gene03  5   20
Gene05  22  40
Gene06  88  2

##</code><code>##

 File1:                  File2: 

 Gene01 5   15          Gene01  12  3
 Gene03 25  5           Gene03  5   20

##</code><code>##

 if ($tmpArray1[0] eq $tmpArray2[0]){
 $commongenes{$tmpArray2[0]} = 
    $tmpArray1[1].':'.$tmpArray1[2].':'.$tmpArray2[1].':'.$tmpArray2[2];
 }

##</code><code>##

 #!/usr/bin/perl -w
 use strict;                    

 my $file1=$ARGV[0];          
 my $file2=$ARGV[1];

 open (FILE1, "<$file1") or die "Cannot open $file1 for processing!\n";        
 open (FILE2, "<$file2") or die "Cannot opent $file2 for processing!\n";      

 my @fileLine1=<FILE1>;   
 my @fileLine2=<FILE2>;   

 my %file1_allgenes=();        
 my %file2_allgenes=();        
 my %commongenes =();


 my ($file1_group0name, $file1_group1name, $file1_group2name)=('','','','');
 my ($file2_group0name, $file2_group1name, $file2_group2name)=('','','','');    

 for (my $i=0; $i<=$#fileLine1 && $i<=$#fileLine2; $i++) {   
 chomp($fileLine1[$i]);                                 
 chomp($fileLine2[$i]);                                 
 my @tmpArray1=split('\t',$fileLine1[$i]);               
 my @tmpArray2=split('\t',$fileLine2[$i]);                  

 if ($i==0) {            ## Column Names and/or Letters
    $file1_group0name=substr($tmpArray1[0],0,6);         
    $file1_group1name=substr($tmpArray1[1],0,4);         
    $file1_group2name=substr($tmpArray1[2],0,4);         
    $file2_group0name=substr($tmpArray2[0],0,6);         
    $file2_group1name=substr($tmpArray2[1],0,4);         
    $file2_group2name=substr($tmpArray2[2],0,4);         
 }
 if ($i!=0) {     ## Concatenated values in 3 separate hashes                                       
    if (! defined $file1_allgenes{$tmpArray1[0]}) {      
        $file1_allgenes{$tmpArray1[0]}=$tmpArray1[1].':'.$tmpArray1[2];  

    }                                       
    if (! defined $file2_allgenes{$tmpArray2[0]}) {     
        $file2_allgenes{$tmpArray2[0]}=$tmpArray2[1].':'.$tmpArray2[2];             

    }
    if ($tmpArray1[0] eq $tmpArray2[0]){
        $commongenes{$tmpArray2[0]} = 
    $tmpArray1[1].':'.$tmpArray1[2].':'.$tmpArray2[1].':'.$tmpArray2[2];
    }

  }
    my @commongenes = %commongenes;               
    print "@commongenes\n\n";              
  }