How to determine similar expression PATTERNS using time course

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7.0 years ago

Hushus ▴ 20

Hey all,

I have the following set of RNA expression data, columns = time in development, rows = individual genes. I would like to know which genes GO UP or DOWN during the 10-12 hr time point based on the flanking time points (4 hrs before and after). What I really want to see is which of these genes steadily increase at the 10-12 hr time point then decrease after wards. In other words, I want to see which genes follow the same PATTERN.

I was thinking of taking time points from 6 to 14 hrs and fitting a non-linear line, getting the equation of that and comparing those with other genes.

Clustering (if I understand it correctly) would not work because im not looking at which genes are HIGHEST or LOWEST at that time point, im looking for which genes exhibit similar expression PATTERNS

Thank you for your time

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RNA-Seq time course pattern • 1.7k views

ADD COMMENT • link 7.0 years ago by Hushus ▴ 20

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See figure 5 here, doesn't clustering allows you to find the desired pattern?

enter image description here

ADD REPLY • link 7.0 years ago by h.mon 35k

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THATS EXACTLY WHAT I WANT!

So just need to use this timecourse program ya?

Thanks a ton

ADD REPLY • link 7.0 years ago by Hushus ▴ 20

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