Done on the Tabula Muris Senis dataset.
Data is raw RNA-seq counts from
https://czb-tabula-muris-senis.s3-us-west-2.amazonaws.com/Data-objects/tabula-muris-senis-facs-official-raw-obj.h5ad
Visualization of the result can be found at https://gos.garden/vis-age/
The visualization code - in https://github.com/justgos/vis-age
Pre-processed as
- RNA counts normalized to 1.0 per cell
Cell statistics (expression mean and std.dev) are calculated - with 4 levels of granularity - on subsets defined by a unique combination of
- Animal sex
- Tissue type
- Subtissue type
- Cell type
Expression fold-changes computed between subsets of the pairs of age groups are filtered as
- Subset has >= 3 cells
- Expression is >= 1e-12 in both age groups
- Bonferroni correction is applied to p-values by multiplying them first by the number of genes (~20k) and then by the number of subsets (2-1000 depending on granularity). Results are then thresholded by 1e-5
Notebooks
- cognitis.ipynb - exploration + systematic analysis of expression fold-changes
- videns.ipynb - preparation of additional pathway data for visualization
All the results for different analysis granularity levels:
- results/merged-cell_ontology_class.csv
- results/merged-subtissue.csv
- results/merged-tissue.csv
- results/merged-sex.csv
- results/merged.csv - total merge across all the granularities