use warnings;
use strict;

my $transvalues = {
  1 => {'gene' => 3},  # sample
  4 => {'gene' => 6}   # data
};

while (my ($key, $row) = each %$transvalues) {
  print "ROW: $key\n";

  while (my ($column, $value) = each %$row) {
    print "  $column => $value\n";
  }

  print "\n";
}

ROW: 4
  gene => 6

ROW: 1
  gene => 3