What have you tried? You haven't demonstrated any effort at solving your own problems. (I presume combine duplicate entries was also posted by you.)

A hash keyed by protein would be useful. The values would be lists of organs. You can use split to seperate the protein from the organ.

You may find the answers to combine duplicate entries helpful as a starting point. During building the hash take note of the number of elements in the largest array. Then iterate from 1 to number of elements. In each iteration use grep to pull out a list of the arrays containing the data for the file matching that number of elements.

my %h;
while ( defined ( $_ = <DATA> )){
  chomp;
  my ( $k, $v) = split ' ';
  push @{$h{$k}}, $v;
}

open my $fh1, '>', '/tmp/1.txt' or die;
open my $fh2, '>', '/tmp/2.txt' or die;

for my $k ( sort keys %h ) {
  my $c = @{$h{$k}};  
  for ( @{$h{$k}}){
    $c > 1 ? print $fh2 "$k\t$_\n" : print $fh1 "$k\t$_\n";
  }}
__DATA__  
protein1   stomach
protein2   head
protein3   muscle
protein3   heart
protein3   brain
protein4   leg
protein5   toes
protein5   mouth
protein6   ear
[download]

while ( defined ( $_ = <DATA> )){
is equivalent to
while ( <DATA> ){

$c > 1 ? print $fh2 "$k\t$_\n" : print $fh1 "$k\t$_\n";
is equivalent to
print { $c == 1 ? $fh1 : $fh2 } "$k\t$_\n";
or do
my $fh = $c == 1 ? $fh1 : $fh2;
outside the loop and print to $fh.

Thanks, I know. I try to write it simple for the newbies.
Boris

#!/usr/bin/perl -w
use strict;

my %hash;
(!/^$/) && (push @{$hash{(split /\s+/,$_)[0]}}, (split /\s+/,$_)[1]) w
+hile(<DATA>);


open TMP1, '>duplicates.txt' or die;
open TMP2, '>distinct.txt' or die;

for my $key (keys %hash) {
   for (@{$hash{$key}}) {
    (@{$hash{$key}} > 1) ? print TMP1 "$key\t$_\n" : print TMP2 "$key\
+t$_\n" ;
   }
}

__DATA__
protein1   stomach
protein2   head
protein3   muscle
protein3   heart
protein3   brain
protein4   leg
protein5   toes
protein5   mouth
protein6   ear
[download]