in reply to creating a matrix like format

Here is a one-liner option: 
>perl -anE "$h{$F[3]}||=$col++; push @x,[$F[0],$h{$F[3]},$F[4]]}{say q
+q|Gene\t\t|,join(qq|\t|,keys %h);for my $r(@x){say qq|$r->[0]\t|,map{
+$h{$_}==$r->[1]?
$r->[2]:qq|\t|} keys %h}" data.2

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Yes - it is a little ugly, but it works.

        This is not an optical illusion, it just looks like one.

In Section Seekers of Perl Wisdom