de2425, this is a fast and dirty rewrite of your code, incorporating some of moritz's and shmem's comments. Further, I'll note you don't get keys from $ING, but rather from the hash %ING. The code below has not been run but it has been checked for syntax with perl -cw. I'll note that most of what I've done is clean up the variable syntax (and I'm sure someone else could do a better job of it).
I've also taken the time to eliminate a lot of those hard coded files and directory settings. The name of the output file can now be passed as a parameter as well.

#!/usr/bin/perl
use warnings;
use strict;

#
# Rewrite for legibility.
# This code is not tested.
#

my $output_file = shift || "Cytokine.txt";
my $work_dir = "c:/work/Cytokine_By_Company";
my $report_dir = "c:/work/GeneID_Count";
my $data_set_one = "ING_cytokines_200805.txt";
my $data_set_two = "CytokineArrays.txt";


my %ING;

open (IN, "< $work_dir/$data_set_one") or
    die "Could not open input file $data_set_one. $!\n";

while (<IN>) {
   chomp;
   my @source_data = split(/\t/,$_);
   $ING{$source_data[8]}{name} = $source_data[0];
   $ING{$source_data[8]}{count} = 0;
}
close IN;

open (OUT, "> $report_dir/$output_file") or 
    die "Could not open file $output_file. $!\n";
open (IN, "< $work_dir/$data_set_two") or 
    die "Could not open file $data_set_two. $!\n";

while(<IN>) {
   chomp;
   my @target_data = split(/\t/,$_);
   my $cytokine_id = $target_data[2];
          
   while (/\d+/ and exists $ING{$cytokine_id}{name}) {
       $ING{$cytokine_id}{count}++;
   }
             
   for my $id ( sort{ $ING{$b} <=> $ING{$a} } keys %ING) {
         print OUT "$ING{$id}{name}\t$ING{$id}{count}\n";
   }
}      
close IN;
close OUT;
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