I would use a hash of lists, instead of a list of lists but it's up to you. Something like this should work:

#!/usr/bin/perl -w

my %data; ## This will be a hash of lists, holding the data
my @names; ## This will hold the names of the columns
while (<>) {
    chomp;
    my @list=split(/\t/); ## Collect the elements of this line
    for (my $i=0; $i<=$#list; $i++) {
        ## If this is the 1st line, collect the names
        if ($.==1) {
            $names[$i]=$list[$i];
        }
        ## If it is not the 1st line, collect the data
        else {
            push @{$data{$names[$i]}}, $list[$i];
        }
    }
}
foreach (@names){
    local $"="\t"; ## print tab separated lists
    print "$_\t@{$data{$_}}\n";
}

If you save the script above as parse.pl and run it on your data, it will print:

$ perl parse.pl data.txt
A    227844250    227824251    227344253    227834254    227834257    227834259    -
B    -    25029365    25029367    25029368    25029370    25029372    25027524
C    38234815    38234816    38234818    38234819    38234822    38234823    -
D    -    -    237786606    237786608    237784891    237786615    -
E    -    19554132    19554134    19554167    23309001    19554173    19552119

Each of your columns can be accessed by name in the script. For example, the column "B" is @{$data{B}}.

Just for fun, you can get the same output as that given by @terdon using an R one-liner:

> Rscript --vanilla -e "write.table(t(read.delim('file.tsv')), col.names=F, quote=F, sep='\\\t')"
A    227844250    227824251    227344253    227834254    227834257    227834259    -
B    -    25029365    25029367    25029368    25029370    25029372    25027524
C    38234815    38234816    38234818    38234819    38234822    38234823    -
D    -    -    237786606    237786608    237784891    237786615    -
E    -    19554132    19554134    19554167    23309001    19554173    19552119

t() is a handy function for this kind of stuff, I realise a Perl array output is what you want—just thought I'd share this anyway.

use an array of arrays and push the result in each using a split function.

http://www.tizag.com/perlT/perlarrays.php

thanks a lot for the suggestions :)