# assume REGEX is the pattern filehandle
# asseme INPUT is the your input filehandle
my %regex=();
while (<REGEX>) {
  chomp;
  my ($key,$value) = split (\t,$_);
  $value = "\"$value\"";
  $regex{$key}=$value;
}

while (<INPUT>) {
  s/$key/$regex{$key}/gee foreach my $key (keys %regex);
}