Your code has quite a few problems and it seems that you are not grasping some fundamental concepts. If you are new to the language I would recommend you pick up a copy of "learning perl". I'm too lazy to comment each line of your code, but I'm sure some kind monk will. A thing which you have to be careful about this particular file is that it uses crlf (windows style) newlines. As I understand it perl automatically accounts for this on windows, but if you're on unix you need to explicitly open the file with "<:crlf".
Some important concepts you should familiarize yourself with:

• Variable references vs Normal variables (perldata)
• Scalar vs List context (perldata)
• Looping constructs in perl (perlsyn)
• Default variables (perlvar)

The list is by no means complete and as mentioned I would recommend getting a good book perl (learning perl or programming perl)

Below is some code which does what you want using what I believe are reasonably good conventions.

Good Luck
Hermes

#!/usr/bin/env perl

#Good practice (prevents autovivification)
use strict; 

my (@x, @y1, @y2, @y3, @y4);

open FILE, '<:crlf', "test.txt";

#Get and store header data
chomp(my $headerline=<FILE>);
my @headerdata=split /\t/, $headerline;


#Process each subsequent line of the file, storing the current line in
+ $_
while(<FILE>) { 
    #Remove newline from $_ (var holding current line)
    chomp; 

    #Split $_ using tab as delimeter and store contents in @rowdata
    my @rowdata=split /\t/; 

    #Store first column of the line in @x, etc..
    push @x, shift @rowdata; 
    push @y1, shift @rowdata; 
    push @y2, shift @rowdata; 
    push @y3, shift @rowdata; 
    push @y4, shift @rowdata; 
}
close FILE;

print "Array headerdata: @headerdata\n";
print "Array x: @x\n";
print "Array y1: @y1\n";
print "Array y2: @y2\n";
print "Array y3: @y3\n";
print "Array y4: @y4\n";
[download]

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