EQ is used in parsing equations embedded in scientific text:
+-----MVa-----+
| +---Xd--+---Xc--+
+----Ss----+---Pvf--+ | +-EQ+-EQ-+ |
| | | | | | | |
Phosphorylation was.v observed.v ( P.eq =.v 0.06 )
The equals sign is marked as =.v because it behaves in a verb-like manner ("the probability is 0.06"). It is also taken to be the expression head, and is the point from which the equation connects to the "outside world", using MX- or MVa- links.
Expression parsing is fairly constrained and weak: equations must appear within parenthesis. Single letters and numbers can appear in equations, as well as nouns, which are treated as "subjects" or "objects". The EQ link is used only in these parenthetical equations; in free text, equals signs, less-than and greater-than signs, and similar are treated as synonnyms for the verb "is". In the example below, the CV link connects to the head verb of the dependent clause, in this case, the equals sign.
+----CV---+
+---TH---+-Cet-+-Ss+Op+
| | | | |
I think that x.n =.v 4
This is similar to how colons are treated:
+-----------------WV----------------+
+------Wd------+---------Ss---------+
| | +--Osm-+
| | | |
LEFT-WALL the capital of Germany :.v Berlin