Show us the input file Table1.txt.
Here you are splitting the input line based on tab delimiter and collecting the first element[0] in  $key 
my $key = (split/\t/, $line)[0];

[download]
Here you are pushing every line that has the same key into an array 
push @{ $hash{$key} }, $line;

[download]
There can only be unique keys in such a data structure. UPDATE 
while(<DATA>)
{
   chomp;
   my $line = $_;
   
   my $key = (split/\s+/, $line)[0];
   push @{ $hash{$key} }, $line;
}

print Dumper(\%hash);

__DATA__
NM_001127328    202502_at
NM_000018    200710_at
NM_000019    205412_at
NM_001111067    203935_at
NM_000023    210632_s_at
NM_000027    204332_s_at
NM_000027    204333_s_at
NM_000027    216064_s_at
NM_000029    202834_at
NM_000031    218487_at
NM_000031    218489_s_at
NM_000032    211560_s_at
NM_000036    206121_at
NM_000042    205216_s_at
NM_000043    204780_s_at
NM_000043    204781_s_at
NM_000043    215719_x_at
NM_000043    216252_x_at
NM_000044    211110_s_at
NM_000044    211621_at

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

[download]

In reply to Re^3: Load a file into hash with duplicate keys by umasuresh
in thread Load a file into hash with duplicate keys by sophix

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