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Lets say I have few genomic regions (Transcription factor binding sites) and I want to know it's target genes. The simplest way is to find the nearest gene to the these genomic regions and check the path way using any GO tools.
My question here is how to fix the window cutoff (The distance between binding sites and nearest gene).
For example
1. lets say 1000 kb. I will take the single nearest gene that fall under 1000 kb.
2. or I will take 2 nearest genes by using + or - 1000 kb upstream or downstream
3. or I use 500 kb upstream and 1000 kb downstream and will take single nearest gene.
But my problem is how much distance I should use as a cutoff ????
My question here is how to fix the window cutoff (The distance between binding sites and nearest gene).
For example
1. lets say 1000 kb. I will take the single nearest gene that fall under 1000 kb.
2. or I will take 2 nearest genes by using + or - 1000 kb upstream or downstream
3. or I use 500 kb upstream and 1000 kb downstream and will take single nearest gene.
But my problem is how much distance I should use as a cutoff ????
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