Folks have already given very detailed answers. I’ll just add a short and simple one: Lots of trial and error.
You cause an error in Gene x and see what changes. Is a protein missing? Or is something over expressed? Then you try and establish the exact mechanisms how the gene causes the effect.
Fun fact: some genes are named after what the cause when they are deactivated. For example the Wuschel gene in plants leads to a change in appearance. “Wuschel” is German and means something like “fluffy” or “hairy”. The plants which had a mutation in this gene, only grew very short stems, leading to a “fluffy” appearance.
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