Tokyo’s subway system…

In order to fully understand the Tokyo metro system, you must first understand that it is run by several different companies: Tokyo Metro (東京メトロ) and Toei (都営) run underground; Japan Railways (JR) cuts through the city; and a multitude of private companies (Keio [京王], Odakyu [小田急], Tokyu [東急]) serve mostly the suburbs. Each of these systems is independent, with unique ticketing schemes and maps.

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(Source: nileguide.com)