SenePy signature from lung

[linpei26]

Hi!

I am interested in lung and its related ageing in gene expression so SenePy look great to me.
My question is that for mouse,
are there currently only 3 predefined gene signature for lung in SenePy (1 for alveolar macrophages and 2 for fibroblast)?
If so, do I need to compile lists of ageing related signature genes for other cell types if I want to look at something beyond fibroblast and macrophages?
Thank you!

[mousepixels]

I recommend trying the universal gene signature. In all our testing, it did an excellent job of broadly characterizing senescence in many different tissues or cell types. You could also try using a similar cell type from a different tissue or a merged signature from multiple similar cell types using the merge function (or alternatively, merge all lung cell signatures). Unfortunately, there were not enough cells from every cell type in every tissue to make a completely comprehensive signature set of every distinct cell type. But the universal one should do a pretty good job! Let us know if you have any questions. Thanks for trying it out!

[linpei26]

Sounds great. Thank you for the helpful message!

[mousepixels]

You can use typical pandas syntax to browse/filter the hubs.metadata dataframe.

For example if you wanted all lung signatures you could do:
hubs.metadata[hubs.metadata.tissue == 'Lung']

If you wanted to find all endothelial cells you could do something like this. Note, that I am doing a contains instead of strict match just in case of pluralization or additional context:
hubs.metadata[hubs.metadata.cell.str.contains('endothelial', case=False)]