Just to give you an idea of how many subway lines criss-cross Tokyo, here is a subway map. This does not include the lines operated by the country's major rail line, Japan Railway (JR), that also serve Tokyo commuters.
Looking at the map you will see a solid oval in the middle of the map. My guess is that this represents the lands of the Imperial Palace in central Tokyo. To the left of that oval, where 3 red lines bend close to one another is Shinjuku station. Actually it looks like there are 5 stations containing the name Shinjuku in that area. Further left, and a little bit up, near the edge of the map is a station labelled Ogikubo. If the map continued to the left the station I will be living near, Nishi-Ogikubo, would be the next one on that subway line.
Oh, and those subway lines are run by different companies.