use strict; 
use warnings;

use List::Util qw(reduce);
use Data::Dumper;


my $hash = 
    reduce { ${ $a->{ $b->[1] } }->{ $b->[2] } = $b->[3]; $a; } 
    {}, grep { @$_ > 3 }    
    map { [ split /\s{2,}/ ] }
    map { chomp; $_ }
    <DATA>
;

print Dumper( $hash );

__DATA__   
1    Sample 1    actin        20,514
2    Sample 1    claudin        30,544
3    Sample 1    occludin        31,183
25    Sample 1    actin        20,514
26    Sample 1    claudin        30,544
27    Sample 1    occludin        31,183
49    Sample 2    actin        20,416
50    Sample 2    claudin        25,611
51    Sample 2    occludin        27,831
73    Sample 2    actin        20,416
74    Sample 2    claudin        25,611
75    Sample 2    occludin        27,831
97    Sample 3    actin        24,213
98    Sample 3    claudin        32,065
99    Sample 3    occludin        34,556
121    Sample 3    actin        24,213
122    Sample 3    claudin        32,065
123    Sample 3    occludin        34,556
145    Sample 4    actin        20,498
146    Sample 4    claudin        25,365
147    Sample 4    occludin        27,869
169    Sample 4    actin        20,498
170    Sample 4    claudin        25,365
171    Sample 4    occludin        27,869
193    H2O    actin        
194    H2O    claudin        
195    H2O    occludin        
217    H2O    actin        
218    H2O    claudin        
219    H2O    occludin
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