In your regex:

$LINE =~ s/($WORD)/<font color=red><b><i>$1<\/i><\/b><\/font>/gi
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You are using ($WORD). This will consider the () to be a group. If you are wanting to find the () as well as the $WORD you need to try this:

$LINE =~ s/\(($WORD)\)/<font color=red><b><i>$1<\/i><\/b><\/font>/gi
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