Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:3
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Sprint:Fall 2 2023 Sep 17, Fall 3 2023 Oct 2
Description
We want to group genes into clusters based on their expression over time, focusing on just the genes that were found to be responsive to the heat stress.
For this task, investigate how we can generate clusters.
For example, there might be some genes that increase expression in response to heat stress in every time point, with bigger increases in later time points.
Or, there might be some genes that don't increase at all until one of the middle points. There are many possible patterns.
Here, we want to identify and cluster genes based on their basic expression patterns or their fold-change patterns.
Cosult with Johnson Lab (Rasha and Sorel) to replicate what they did for their very similar time course data set.
Ann suggests looking at "mufz" https://www.bioconductor.org/packages/release/bioc/html/Mfuzz.html
An RShiny tool for mfuz: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8825645/
Attachments
Activity
This is now been consumed by IGBF-I 3454 and has been made redundant.
Related to this, is IBGF-3454.
It will test out EB-Seq and see how well it clusters.
It might solve much of this task!