Viktor Petukhov PRO
PhD student at the University of Copenhagen
Case-control analysis of single-cell RNA-seq studies
Petukhov V, Igolkina A, Rydbirk R, Mei S, Christoffersen L, Kharchenko P, Khodosevich K
viktor.petukhov@pm.me
Description of the problem
Two conditions, multiple samples per condition, multiple cells per sample
Case samples
Control samples
What can we possibly do?
Gene expression analysis
Compositional analysis
Cluster-based
Cluster-free
control
epilepsy
Case-control analysis of single-cell studies: a fresh approach
What can we possibly do?
Gene expression analysis
Compositional analysis
Cluster-based
Cluster-free
control
epilepsy
Case-control analysis of single-cell studies: a fresh approach
Expression analysis, cluster-based
What cell types are affected the most?
D = \frac{d_{between}}{\overline{d_{within}}}
Expression analysis, cluster-based
Simulation data (muscat)
Sensitivity
Dependency on the number of cells
*Thanks to Lars Christoffersen!
Expression analysis, cluster-based
Updated formulas
Old
New
P-values
Updated formulas
Stricter filtration
Expression analysis, cluster-based
PCA in the pre-processing
Count data
PCA
Expression analysis, cluster-based
Select genes, most different between conditions
Count data
Top 1000 DE genes
Expression analysis, cluster-based
Select genes, most different between conditions
Count data
Top 1000 DE genes + PCA
Expression analysis, cluster-based
Select over-dispersed genes
Count data
Top 500 OD genes
Expression analysis, cluster-based
Autism, count data
Expression analysis, cluster-based
Autism, PCA
Expression analysis, cluster-based
Autism, 500 DE genes
Expression analysis, cluster-based
Autism, 500 DE genes, PCA
Expression analysis, cluster-based
Epilepsy, count data
Expression analysis, cluster-based
Epilepsy, PCA
Expression analysis, cluster-based
Epilepsy, 500 DE genes
Expression analysis, cluster-based
Epilepsy, 500 DE genes, PCA
Expression analysis, cluster-based
MS, variation analysis, 100 OD genes
*not adjusted p-values!
Expression analysis, cluster-based
MS, variation analysis, 100 OD genes, exclude sex-related genes
*not adjusted p-values!
Expression analysis, cluster-based
MS, variation analysis, 100 OD genes, exclude sex-related genes
*not adjusted p-values!
Expression analysis, cluster-based
MS, variation analysis, scITD
*https://github.com/kharchenkolab/scITD by Jonathan Mitchel
Expression analysis, cluster-based
MS, variation analysis, scITD
*https://github.com/kharchenkolab/scITD by Jonathan Mitchel
What can we possibly do?
Gene expression analysis
Compositional analysis
Cluster-based
Cluster-free
control
epilepsy
Case-control analysis of single-cell studies: a fresh approach
Expression analysis, cluster-free
Epilepsy, global programs
Expression analysis, cluster-free
SCC, local programs
Expression analysis, cluster-free
SCC, local program GOs
Expression analysis, cluster-free
SCC, local program GOs
Expression analysis, cluster-free
SCC, local program GOs
Thank you!
Konstantin Khodosevich lab
Peter Kharchenko
- Rasmus Rydbirk
- Anna Igolkina
- Shenglin Mei
- Lars Christoffersen
Co-authors
viktor.petukhov@pm.me
Jonathan Mitchel
*No photo :(
Cacoa, PM KK Aug 2021
By Viktor Petukhov
