use Inline::Files;

/(Gene\d+)/ and undef $a[0]->{$1} for <LIST>;

while($e++ < 3 and  $f = 'FILE'.$e) {
	/(Gene\d+)/ and undef $a[$e]->{$1} for <$f>;
}

foreach $k (sort keys %{$a[0]}){
	print "$k\t", join(' ', map {exists $a[$_]->{$k} ? 1 : 0} 1..$#a),"\n";
}



__LIST__
Gene1
Gene2
Gene3
Gene4
Gene5
Gene6
__FILE1__
Gene1
Gene2
Gene3
__FILE2__
Gene2
Gene3
Gene4
__FILE3__
Gene3
Gene4
Gene5
Gene6