Are any of the 3 main features in the paper associated with mRNA levels of genes

shntnu commented 3 years ago

[ ] Cytoplasm_AreaShape_Zernike_9_3
[ ] Cells_RadialDistribution_RadialCV_Mito_1of4
[ ] Cytoplasm_Granularity_3_RNA

Are any of these 3 CellProfiler features involved in predicting any of the well-predicted genes in our paper? If so, what gene(s) do they predict?

@AnneCarpenter I wonder if we also need to go in the other direction i.e. are any of these well predicted and if so, what are the genes that best predict them?

(WASF2) Cytoplasm_AreaShape_Zernike_9_3
(PRLR) Cells_RadialDistribution_RadialCV_Mito_1of4
(TSPAN15) Cytoplasms_Granularity_3_RNA

AnneCarpenter commented 3 years ago

Yes, exactly so - both directions though I apparently mistakenly thought it was symmetrical.

shntnu commented 3 years ago

@MarziehHaghighi can you please help figure this out?

MarziehHaghighi commented 3 years ago

@shntnu you can see important genes for prediction of the three mentioned features. I also see three genes in parentheses. What is the meaning of that map between that CP features and Genes?

broadinstitute / cmQTL

Are any of the 3 main features in the paper associated with mRNA levels of genes #67

Cytoplasm_AreaShape_Zernike_9_3

Cells_RadialDistribution_RadialCV_Mito_1of4

Cytoplasm_Granularity_3_RNA