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# Strict
use strict;
...
    my $pvalues = $output{$id};
    printf "%12.12s | %s\n", $id, join(" | ", @$pvalues);
}

      gene 1 | value 1.1 | value 1.1 | value 1.2
      gene 2 | value 2.1 | n.a. | n.a.
      gene 3 | n.a. | value 3.1 | value 3.2
      gene 4 | value 4.1 | value 4.1 | value 4.2
      gene 8 | value 8.1 | n.a. | n.a.