This is something I'd probably use Set::Scalar for. It does all the set stuff for you.

$hash{g1} = Set::Scalar->new(qw(ATG1 ATG2 ATG4 ATRG7));
$hash{g2} = Set::Scalar->new(qw(ATG1 x y z));

if( $hash{g1}->intersection($hash{g2}) ) {
    print "merging g1 and g2\n";
    $hash{g1}->insert(delete $hash{g2})
}
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Not sure if that really answers the question though.