Given that you have two sets of non-numeric keys, I would think a hash of hashes is a more logical structure than a hash of arrays. I would also, as Athanasius suggests, separate your data structure construction from your output process. Essentially, build a hash of hashes, create sorted lists of your genes and transcription factors, and then print the table:

#!/usr/bin/perl
use strict;
use warnings;
use List::MoreUtils qw(uniq);
use 5.10.0;

my %gene2TF2val;
while (<DATA>) {
    my ($gene, $tf) = split;
    $gene2TF2val{$gene}{$tf}++;
}

# ID distinct transcription factors, sorted by value
my @tf = sort { ($a =~ /(\d+)/)[0] <=>  ($b =~ /(\d+)/)[0]} 
         uniq map keys %$_, values %gene2TF2val;

# Print table header
say join "\t", "NAMES", @tf;


# Print table contents
for my $gene (sort keys %gene2TF2val) {
    say join "\t", 
        $gene, 
        map $_ ? '+' : '-', 
            @{$gene2TF2val{$gene}}{@tf};
}


__DATA__
geneA    T1
geneA    T1
geneA    T2
geneB    T8
geneC    T10
geneC    T1
[download]

Note that the command line switch -w is (mostly) synonymous with use warnings. If you are not yet comfortable with map and Slices, you can store intermediate results in arrays:

#!/usr/bin/perl
use strict;
use warnings;
use List::MoreUtils qw(uniq);
use 5.10.0;

my %gene2TF2val;
while (<DATA>) {
    my ($gene, $tf) = split;
    $gene2TF2val{$gene}{$tf}++;
}

# ID distinct transcription factors, sorted by value
my @tf;
for my $tf (values %gene2TF2val) {
    push @tf, keys %$tf;
}
@tf = sort { ($a =~ /(\d+)/)[0] <=>  ($b =~ /(\d+)/)[0]} 
      uniq @tf;

# Print table header
say join "\t", "NAMES", @tf;

# Print table contents
for my $gene (sort keys %gene2TF2val) {
    print $gene;
    for my $tf (@tf) {
        my $has = $gene2TF2val{$gene}{$tf} ? '+' : '-';
        print "\t$has";
    }
    print "\n";
}


__DATA__
geneA    T1
geneA    T1
geneA    T2
geneB    T8
geneC    T10
geneC    T1
[download]

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