Fine vs coarse cell annotation on lung dataset

[emdann]

Compare targets with single-cell evidence for coarse vs fine uniformed cell annotations using lung samples/diseases, comparing ontology based coarse annotations with annotations from Extended Lung cell atlas.

• Are the same genes identified as cell type markers and disease cell type markers?
• Are more successful targets identified when testing on fine grained annotation?

[emdann]

• Select diseases: using pneumonia, cystic fibrosis, COPD and PF where samples are all in HLCA, and mix of cases with and without strong sc svidence enrichment (to test if fine annotation leads to finding more targets)
• Download HLCA data with fine & uniform annotations and pseudobulk
• Run DE analysis on HLCA pseudo-bulk annotations
• Compare enrichment on selected diseases
• Compare set of targets identified for different diseases

[emdann]

Another idea for fine vs coarse comparison: using celltypist organ models