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;