Electronic equipment is distributed at several locations known as electrical compartments, avionics bays, or other similar names, where elements are interconnected and cooled. The different pieces of equipment (line replaceable units / LRU in engineering parlance) are then connected to the cockpit, or to other locations, using the avionics network.
LRU are placed in standard racks. In general these compartments can only be accessed while on the ground through a door at the bottom of the fuselage.
On the B737 NG (-600/-700/-800/-900) there are several racks at the level of the cargo bays, a bit aft of the nose wheel gear:
Source: B737 NG, General Familiarization Manual.
Boeing uses ATC to refer to the transponder. There are two ATC electronic units, both in rack E1. Layout of rack E1:
Source: B737 NG, General Familiarization Manual.
Rack E1 on a B737-800 (without the top shelf):
Source: Airliners.net, photo by Petr Volek
A transponder looks like this (Collins TPR-901):
Source: Collins Aerospace.
There are two connectors on the back panel for the top and bottom antennas (ATC antennas location), and two connectors for the network. This model can be seen on this other avionics bay, for a B737-700 (sorry for the terrible quality):
Source: digi.no.
More: How are electronic systems locked and connected in the electronic bay?
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