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open (CYT, "C:/Work/ING_Occurrences_Companies/CytokineArrays.txt");

open (CYT, "C:/Work/ING_Occurrences_Companies/CytokineArrays.txt")
    or die "can't read 'C:/Work/ING_Occurrences_Companies/CytokineArra
+ys.txt': $!\n";

use strict;
my $cytok_file = "C:/Work/ING_Occurrences_Companies/CytokineArrays.txt
+";
open CYT, '<', $cytok_file or die "can't read '$cytok_file': $!\n";

     while (<CYT>){
     chomp;
     @cytokine=split(/\t/,$_);}

while (<CYT>) {
    chomp;
    my ($name, $description, $ID ) = split /\t/;
    $occurrences{$ID} = 0;  # initial count
}

while (<CYT>) {
    chomp;
    my $ID = (split /\t/)[2];
    $occurrences{$ID} = 0; # initial count
}

while (<CYT>) {
    chomp;
    $occurrences{ (split /\t/)[2] } = 0; # initial count
}

close CYT;

close CYT or die "can't close filehandle CYT properly: $!\n";

open (OUT, ">C:/Work/ING_Occurrences_Companies/ING_Count.txt"); 
open (IN, "C:/Work/ING_Occurrences_Companies/ING.txt");

my $outfile = "C:/Work/ING_Occurrences_Companies/ING_Count.txt";
my $infile  = "C:/Work/ING_Occurrences_Companies/ING.txt";

open OUT, '>', $outfile or die "can't write '$outfile': $!\n"; 
open IN,  '<', $infile  or die "can't read '$infile': $!\n";

     while (<IN>){
     chomp;
...
     print OUT "$ING[0]\t$ING[1]\t$cytokine{$ING[2]}\t$count\t\n";

}}

my %lines;
while (<IN>) {
...
    $ocurrences{$ID}++;
    $lines{$ID} = $_;
}

foreach my $ID (sort keys %ocurrences) {
    print $lines{$ID}, "\t", $ocurrences{$ID}, "\n";
}