Your first segment will get always undefs or whatever happens to be lying around in $1,$2,$3 because the 'do' in a 'do/while' loop is always executed once before the first time the while expression is tested for a match. You probably want to change this into a normal while loop like this:

my $ranking_dgp = 0;
while ( $text =~ m{gene\=(ENSG\d+).*?<TD>\s+(\d+|X|Y)\s+</TD>.*?
<TD>.*?<TD>.*?<TD>.*?<TD>\s(\d.\d+)\s\<\/TD\>}gsm){
       my  $gene       = $1;
       my  $chromosone = $2;
       my  $score_dgp  = $3;
       $ranking_dgp = $ranking_dgp + 1;
        push @gene_score, [ $gene, $chromosone, $score_dgp, $ranking_d
+gp ];
    }

print Dumper @gene_score;
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