#!/usr/bin/perl
use strict;
use warnings;

my $file1 = <<FILE1;
GRB2
AFF4
GGGB
C7orf42
FILE1
my $file2 = <<FILE2;
KEGG_PATHWAY	hsa04722:Neurotrophin signaling pathway	33	0.14786271171251902	4,04E+09	GRB2, CAMK2G, NFKB1, MAPKAPK2, MAGED1, KRAS, MAP3K3, MAP3K1, BCL2, RAC1, GAB1, RHOA, CAMK2D, SH2B3, NGFRAP1, SHC1, MAP2K7, FRS2, PIK3R1, IRS2, RELA, YWHAB, YWHAE, TP73, NRAS, MAPK1, CRKL, JUN, NTRK2, CALM3, MAPK9, SORT1, RAP1A	575	124	5085	2.353.506.311.360.440	6,83E+11	6,83E+11	0.00492932423403758
KEGG_PATHWAY	hsa05200:Pathways in cancer	63	0.2822833587239	1,86E+10	FGF18, FGF5, PPARD, FGF9, NFKB1, FGF13, PTEN, CCNE2, ACVR1B, MAX, CDKN2B, RHOA, RALB, RALA, FAS, TPR, CHUK, RELA, RXRA, LEF1, CDK6, RB1, STK4, DAPK1, JUP, MAPK1, CCDC6, CRKL, HIF1A, NCOA4, JUN, VEGFA, MAPK9, TRAF1, WNT5A, APC2, XIAP, GRB2, IGF1R, KRAS, ITGAV, BCL2, RAC1, RUNX1, PIK3R1, APC, CEBPA, COL4A4, FZD8, COL4A1, IL8, VHL, CREBBP, TGFBR2, SMAD2, FZD5, STAT3, NRAS, RASSF5, CDKN1B, ITGA6, RASSF1, JAK1	575	328	5085	16.985.949.098.621.400	0.003142334832759053	0.0010485440045103767	0.02269450903600312
KEGG_PATHWAY	hsa04310:Wnt signaling pathway	35	0.15682408817994445	4,76E+10	WNT5A, PPARD, APC2, PPP2R5A, CAMK2G, PPP2R5C, PPP3R1, RAC1, NFAT5, PPP3CB, RHOA, CAMK2D, FRAT2, PRKACA, CHP, PLCB1, FBXW11, APC, FZD8, VANGL1, NLK, VANGL2, CREBBP, LEF1, SMAD2, FZD5, SENP2, SFRP5, SFRP1, CCND2, CSNK1E, JUN, MAPK9, SIAH1, PPP2R5E	575	151	5085	20.498.128.419.234.000	0.008008272140318184	0.002008108692225119	0.05796850410908494
FILE2

open my $in1, '<', \$file1;

my @keyWords;

while (defined (my $line = <$in1>)) {
    chomp $line;
    push @keyWords, $line;
}
close $in1;

die "No keywords specified\n" if ! @keyWords;

my $match = "\\b\Q" . join ("\E\\b|\b\Q", @keyWords) . "\E\\b";

open my $in2, '<', \$file2;

while (defined (my $line = <$in2>)) {
    next if $line !~ /($match)/;

    print "Matched $1 in line $.\n";
}

##</code><code>##

Matched GRB2 in line 1
Matched GRB2 in line 2