Actually, I think you would be better off solving this problem with Excel - it is possible to write macros that would do this.

You are going to be on a very steep learning curve with Perl. But to get you started, I would create a hash table out of file2. This will allow you to translate any TID into the SPNAME. Code below. Note how I limited the number of things coming out of the split(). You will need that technique to parse the first file, except there will be 3 fields instead of 2.
 my ($gid,$tid,$concat) = split(/\s+/,$_,3);

#!/usr/bin/perl -w
use strict;
use Data::Dumper;

my %tid2spname;

foreach (<DATA>)
{
   chomp;
   my ($tid, $txt) = split(/\s+/,$_,2);
   $tid2spname{$tid} = $txt;
}

print Dumper \%tid2spname;

__DATA__
10090   Mus musculus
10116   Rattus norvegicus
148305  Magnaporthe grisea
28985   Kluyveromyces lactis
33169   Eremothecium gossypii
3702    Arabidopsis thaliana
4530    Oryza sativa
4896    Schizosaccharomyces pombe
4932    Saccharomyces cerevisiae
5141    Neurospora crassa
5833    Plasmodium falciparum
6239    Caenorhabditis elegans
7165    Anopheles gambiae
7227    Drosophila melanogaster
7955    Danio rerio
9031    Gallus gallus
9598    Pan troglodytes
9606    Homo sapiens
9615    Canis lupusfamiliaris
9913    Bos taurus

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In reply to Re: Multiple loops and comparisions by Marshall
in thread Multiple loops and comparisions by sundeep

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