`cat file` is maybe slower, maybe not good style, but gives you list of lines from without having to bohter about open, close and so on. But if you need such precise control -- let somebody else do it -- that is Path::Tiny.

#!/usr/bin/perl -CSDA 

use utf8;
use Modern::Perl;
no warnings qw{uninitialized};
use Data::Dumper;
use Path::Tiny;

my %myhash =
        map { ($$_[0], $$_[2]) }
        map { [split /\s+/, $_] }
        `cat myfile`;                  # maybe slower, but don't care 
+about open
        # path("myfile")->lines_utf8;  # very reliable

print Dumper(\%myhash); 





result: 

$VAR1 = {
          'AC067940.1' => 'up',
          'CCT5P2' => 'up',
          'GeneName' => 'Regulation',
          'C20orf204' => 'up',
          'NANOS3' => 'up',
          'MIR200A' => 'down',
          'SREK1IP1P1' => 'down',
          'AC091607.1' => 'up',
          'CYP2C8' => 'down',
          'AL662791.1' => 'up',
          'FAR1P1' => 'NA',
          'MIR200B' => 'down',
          'CHTF8P1' => 'NA',
          'RPL19P20' => 'up',
          'MIR429' => 'up',
          'APOL4' => 'up',
          'CFL1P4' => 'down',
          'NAALADL2' => 'NA'
        };
[download]

counting:

 

#!/usr/bin/perl -CSDA 

use utf8;
use Modern::Perl;
no warnings qw{uninitialized};
use Data::Dumper;
use Path::Tiny;

my %count;
$count{$_}++ for
        map { $$_[2] }
        map { [split /\s+/, $_] }    
        path("myfile")->lines_utf8;

print Dumper(\%count);



$VAR1 = {
          'down' => 5,
          'NA' => 3,
          'up' => 9,
          'Regulation' => 1
        };
[download]