Introduction
if you don't know the Tor Network and the Tor Project (but even if you know them), I suggest you read the information from here:
Wikipedia: Tor Anonimity Network
Transparent proxy is an intermediary system that sit between a user and a content provider. When a user makes a request to a web server, the transparent proxy intercepts the request to perform various actions including caching, redirection and authentication.
Transparent proxy via Tor means that every network application will make its TCP connections through Tor; no application will be able to reveal your IP address by connecting directly.
For more information about the Transparent Proxy through Tor please read the Tor Project Wiki.