Regarding applying Gene Set Analysis for determining underlying biological traits in Single Cell Sequencing
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Kasper Thystrup Karstensen
Jun 12, 2017, 2:47:45 PM6/12/17
to Single Cell Biology
So first up, Hi I am a master's student, and are currently writing my thesis regarding learning biology from analysing pathways in Single Cell sequencing.
While examining this subject, I ran into the principles behind Gene Set Enrichment Analysis (GSEA). Thus I planned to perform this analysis on my chosen dataset (10x genomics 3k PBMC dataset - https://support.10xgenomics.com/single-cell-gene-expression/datasets (requires mail, name and institution info, to download dataset). Unfortunately the GSEA methods I have encountered, requires additional phenotypic data (like disease groups data Vs healthy groups data), which to my extend, is not available for the single cell data set I work with.
I post here because I want to hear your thoughts on how to perform Gene Set Analysis and maybe to get some advice, from someone who perhaps have been working with something similar.
Thank you for time, and your thoughts!
Kind regards
- Kasper
While examining this subject, I ran into the principles behind Gene Set Enrichment Analysis (GSEA). Thus I planned to perform this analysis on my chosen dataset (10x genomics 3k PBMC dataset - https://support.10xgenomics.com/single-cell-gene-expression/datasets (requires mail, name and institution info, to download dataset). Unfortunately the GSEA methods I have encountered, requires additional phenotypic data (like disease groups data Vs healthy groups data), which to my extend, is not available for the single cell data set I work with.
I post here because I want to hear your thoughts on how to perform Gene Set Analysis and maybe to get some advice, from someone who perhaps have been working with something similar.
Thank you for time, and your thoughts!
Kind regards
- Kasper
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