my @genes = qw( Gene1 Gene2 Gene3 Gene4 Gene5 Gene6 );

my @raw_files = (
  "Gene1 Gene2 Gene3",
  "Gene2 Gene3 Gene4",
  "Gene3 Gene4 Gene5",
);

my @gene_in_files = map {
  my %content;
  @content{ split " ", $_ } = ();
  \%content;
} @raw_files;

my @gene_matrix = map {
  my $gene = $_;
  [ map { ~~exists $_->{$gene} } @gene_in_files ]
} @genes;

print "Gene", $_+1, " @{$gene_matrix[$_]}\n" for 0 .. $#gene_matrix;

##</code><code>##

Gene1 1 0 0
Gene2 1 1 0
Gene3 1 1 1
Gene4 0 1 1
Gene5 0 0 1
Gene6 0 0 0

##</code><code>##

<code>
[shift-insert, to paste output from my terminal]
</code>

##</code><code>##

my @genes = qw( Gene1 Gene2 Gene3 Gene4 Gene5 Gene6 );

my @raw_files
  = ( "Gene1 Gene2 Gene3", "Gene2 Gene3 Gene4", "Gene3 Gene4 Gene5" );

my $gene_num = 1;
print "Gene", $gene_num++, " @{$_}\n" for sub {
  my @in_file = map { { map { $_ => 0 } split " ", $_ } } @{+shift};
  map {
    my $gene = $_;
    [ map { ~~exists $_->{$gene} } @in_file ]
  } @{+shift};
}->( \@raw_files, \@genes );