As AnonymousMonk suggested, I used the second colum as the key.

#!/usr/bin/perl -w
use Data::Dumper;

my $data = '/Data/Table1.txt'; 
open INFILE, '<', $data or die "aa\n";

my %hash = map { chomp; split /\t/ } <INFILE>;
print Dumper(\%hash);

my $data2 = '/Data/Table2.txt'; 
open INFILE2, '<', $data2 or die "aa\n";

my %hash2;
while(<INFILE2>)
{
   chomp;
   my $line = $_;
   
   my $key = (split/\t/, $line)[0];
   push @{ $hash2{$key} }, $line;
}

print Dumper(\%hash2);

[download]

This returns the following output

$VAR1 = {
          '218489_s_at' => 'NM_000031',
          '216064_s_at' => 'NM_000027',
          '218487_at' => 'NM_000031',
          '211110_s_at' => 'NM_000044',
          '204333_s_at' => 'NM_000027',
          '210632_s_at' => 'NM_000023',
          '203935_at' => 'NM_001111067',
          '211560_s_at' => 'NM_000032',
          '204332_s_at' => 'NM_000027',
          '215719_x_at' => 'NM_000043',
          '204780_s_at' => 'NM_000043',
          '202834_at' => 'NM_000029',
          '206121_at' => 'NM_000036',
          '204781_s_at' => 'NM_000043',
          '205412_at' => 'NM_000019',
          '216252_x_at' => 'NM_000043',
          '205216_s_at' => 'NM_000042',
          '211621_at' => 'NM_000044',
          '200710_at' => 'NM_000018',
          '202502_at' => 'NM_001127328'
        };
$VAR1 = {
          '211560_s_at' => [
                             '211560_s_at       P       P       P     
+  A
P       P       P'
                           ],
          '204332_s_at' => [
                             '204332_s_at       P       P       A     
+  P
P       P       P'
                           ],
          '216064_s_at' => [
                             '216064_s_at       P       M       P     
+  P
P       A       A'
                           ],
          '200005_at' => [
                           '200005_at   P       P       A       P     
+  P
P       A'
                         ],
          '211110_s_at' => [
                             '211110_s_at       P       A       P     
+  A
P       A       P'
                           ],
          '200003_s_at' => [
                             '200003_s_at       P       A       P     
+  P
P       A       P'
                           ]
        };

[download]

The first value elemant in the second hash includes the key.

In reply to Re^4: Load a file into hash with duplicate keys by sophix
in thread Load a file into hash with duplicate keys by sophix

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