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The scope of this question is too wide to be answered on Biology SE. However I will give you very brief answers to your questions (as I have rephrased them) and point you towards some sources of basic information on the Internet. After reading these you may wish to return with more specific questions. I have also briefly summarized some of the problems which ...


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"Note that interaction effects among genes also depend on their physical distance." I think that's more of a pragmatic assumption, because we tend to associate regulatory features with their closest downstream TSS, though it's certainly not a hard and fast rule. e.g., in certain organisms like budding yeast, its known that the most transcription factor ...


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This is an open-ended question and will be impossible to correctly answer. I am voting "to close as too broad". Note also that the question in the title is not the same as the question in the post. But I still wanted to give you some information that may help you. Here are just a few examples for which knowing gene density matters. Background selection ...



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