Here's one way - construct another hash:

#!/usr/bin/perl

use strict;
use warnings;
use Data::Dumper;

my %hash = map {split /\s+/} <DATA>;

my %new_hash;
for my $key (keys %hash){
  if ($key =~ /213119_at/){
    $new_hash{$hash{$key}}++;
  }
}

print Dumper \%new_hash;

__DATA__
Affy:HG_U133A:213119_at:74:303;         ENSG00000123643
Affy:HG_U133A:213119_at:542:439;        ENSG00000123643
Affy:HG_U133A:213119_at:658:369;        ENSG00000123643
Affy:HG_U133A:213119_at:199:255;        ENSG00000123643
Affy:HG_U133A:213119_at:436:453;        ENSG00000123643
Affy:HG_U133A:213119_at:324:381;        ENSG00000458158
Affy:HG_U133A:213119_at:584:557;        ENSG00000123643
Affy:HG_U133A:213119_at:234:507;        ENSG00000123643
Affy:HG_U133A:213119_at:482:429;        ENSG00000123643
Affy:HG_U133A:213119_at:608:451;        ENSG00000458158
Affy:HG_U133A:213119_at:356:297;        ENSG00000123643
[download]

output:

---------- Capture Output ----------
> "C:\Perl\bin\perl.exe" _new.pl
$VAR1 = {
          'ENSG00000123643' => 9,
          'ENSG00000458158' => 2
        };

> Terminated with exit code 0.
[download]

note: there are 9 :-)