Indie Development - Inference in Games and how to Apply it to my own

Whilst designing my game, I got so into the idea of creating my own prototype and getting it to work I didn't think about the theme, Inference. This got me thinking about what ways I could include inference into my runner game instead of jumping head first into it and not taking the theme into consideration.
I started playing games to see in what ways they use inference if any at all, more specifically a game on the Xbox called 'Remember Me' and 'Skyrim'. Remember Me is a game set in the future where you are a memory hunter (a futuristic assassin that steals memories from people or alters them) very similar Mirrors Edge with the parkour element but involves a fully customisable combat aspect to it also. I started playing the game and noticed that on walls this same phrase kept popping up 'train brain train pain' and was only in the slums area of the city where people who had lost all of their memories lived. In further parts in the game as well, seeing this phrase lets you know that you are in the slum area of the city since this phrase isn't seen anywhere else.

As for Skyrim inference is much more abundant one example is for letting the player know about what enemies are going to appear as they tend to hint this quite a lot to the player. When you are entering an area filled with Bandits, they always tend to have spikes or skulls on spikes outside of the cave or castle entrance showing you the types of players that will appear there. Bandit hideouts also contain traps where they hang bones from string making a sound to alert them if you walk into it, as far as im aware no other creature in the game does this.
For the mana and stamina bar, when they reach empty they slowly pulsate and glow making a sound to idicate you have to none left, this is especially useful for players who are in the middle of combat and cant check their mana/stamina because they are too into the current situation at hand, the sound effect is easy to recognise.