G'day Anupam,

This does what you asked for:

#!/usr/bin/env perl

use strict;
use warnings;
use autodie;

use List::Util qw{max};
use Tie::File;

my $master_list = 'pm_1079097_List';
my @files = qw{pm_1079097_File1 pm_1079097_File2 pm_1079097_File3};

tie my @list, 'Tie::File', $master_list;
my %matrix = map { $_ => {} } @list;
untie @list;

for my $filename (@files) {
    tie my @file, 'Tie::File', $filename;

    for (@file) {
        $matrix{$_}{$filename} = 1 if exists $matrix{$_};
    }

    untie @file;
}

my $format = '%' . max(map length, keys %matrix) . 's'
            . ((' %' . max(map length, @files) . 's') x @files) . "\n"
+;
printf $format, '', @files;

for my $gene (sort keys %matrix) {
    printf $format, $gene, map { $_ || 0 } @{$matrix{$gene}}{@files};
}
[download]

Output:

      pm_1079097_File1 pm_1079097_File2 pm_1079097_File3
Gene1                1                0                0
Gene2                1                1                0
Gene3                1                1                1
Gene4                0                1                1
Gene5                0                0                1
Gene6                0                0                0
[download]

I prefixed the filenames you gave with 'pm_1079097_', replace those with your real filenames. The input data I used should match your sample data: it's shown in the spoiler below.

All code I used is documented in http://perldoc.perl.org/perl.html. If you don't understand something, that you should be the first place you look.

If you have follow-up questions, ensure they're accompanied by code, data, error messages, and so on (marked up appropriately, e.g. within <code>...</code> tags) as described in "How do I post a question effectively?".

$ cat pm_1079097_List
Gene1
Gene2
Gene3
Gene4
Gene5
Gene6
[download]

$ cat pm_1079097_File1
Gene1
Gene2
Gene3
[download]

$ cat pm_1079097_File2
Gene2
Gene3
Gene4
[download]

$ cat pm_1079097_File3
Gene3
Gene4
Gene5
[download]