Entering edit mode
10.0 years ago
gillspoor
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0
I have a gene say roughly 5000 nt long and I am looking to see if these particular motifs are atypically expressed in a region of that gene that is around 100nt long. I have stumbled across arlequin, do you know if/how this will tell me if the increased motif pattern in this 100nt fragment is disproportionately expressed? (looking to hopefully be able to declare stat significance - but not sure how achievable that will be given sample size). If someone could give me a spoon-feeding session on how to do this I would be delighted
Many thanks,
Gill
What data do you have? How could a motif be more expressed than the gene that it a part of (I'm just misunderstanding your question, I'm sure)?
Sorry for it being a little 'pigeon -like' I've switched over from psychology - so this is out of my comfort zone. Anyway, I have the whole gene and then I am specifically looking at a part of that gene that is 100nt long. I want to see if the particular motifs I am looking at are disproportionately found in that 100 long part of the sequence compared to the rest of the gene. I have looked in different species and have found the same phenomenon and really could use a way of showing this isn't just random. - to try and be a little more clear - say there are 50% of a particular motif for the entire gene found just in the 100nt stretch I am looking at (that would clearly be at odds with random distribution) - looking for some way of showing this sort of thing is unlikely to happen by chance.
And what are your "data"? Do you know the exact locations of the motif within your gene? In other words, can you answer the question "how many motif instances are within the 100nt and how many are outside it?" And how long is your motif?