Hank Cheng 2024-10-30
git clone https://github.com/yhhc2/Iso-seq_public.gitDetailed usage information will be added soon.
This package takes in data from bulk-Isoseq processed with and without cycloheximide (CHX), a nonsense mediated decay inhibitor (NMDi), and identifies isoforms and genes that are differentially expressed and/or undergoing NMD.
Prior to using this package, the following data processing needs to be performed on bulk Isoseq data:
The package then takes the result from de novo isoform discovery and joint isoform calling to evaluate each isoform and gene in each individual to see if it is undergoing significant and unique functional effects:
- 1. Nonsense mediated decay (NMD): isoforms/genes expressed higher with CHX compared to non-CHX.
- 2. Expression outlier: differentially expressed (gain or loss of expression) isoforms/genes compared to control individuals.
- 3. Allelic Imbalance: genes with haplotype-specific gain or loss of expression.
Please refer to these slides for specifics on the ranking approach with examples:
Statistical approach slides with examples
If the presentation is not opening properly, please try using a different browser or using an incognito window.
To validate the effects of CHX, PCA was performed on the gene-level and isoform-level expression matrix for the 18 patients (36 samples) included in the analysis. The clusters are being formed based on CHX treatment, which supports the idea that sample variability is not enough to prevent us from pulling out findings that are a result of the CHX treatment.
Please visit this site to see an example of how to more interactively visualize the results: http://multiome.brotmanbaty.org/app_direct/multiome-browser/#
This package is developed during my time at the University of Washington as a Genome Sciences graduate student in the Stergachis Lab. Acknowledgements to:
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Andrew Stergachis
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Adriana Sedeno Cortes
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Daniela Witten
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More to be added soon