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theislab / scvelo

RNA Velocity generalized through dynamical modeling
https://scvelo.org
BSD 3-Clause "New" or "Revised" License
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Estimate effect gene perturbation #132

Closed jipeifeng closed 4 years ago

jipeifeng commented 4 years ago

Hi: Thank you for the helpful tool. I have sequenced two data sets (WT vs KO) using 10 x genomics. My question is can I estimate the effect of gene perturbation in the KO data set. My previous observation is that after gene knockdown, the ratio of some cell type decreased, while other cell type increased. Therefore, I want to use the RNA velocity tool to investigate the effect the gene perturbation. My expectation is that we can observe the changes of cell fate of some cell types. Thank you very much! Looking forward to your response!

Peiefeng

VolkerBergen commented 4 years ago

Following the conservation in https://github.com/theislab/scvelo/issues/142 you can apply a DE test on velocity expression to then quantify e.g. scaled difference in expression for DE genes that characterize the temporal dynamics in a particular group. Further gene likelihoods obtained from the dynamical model can be used to assess their significance w.r.t. splicing dynamics.

For further research, it'd be exciting to have a model (e.g. VAE) that learns to generalize the response in stimulation in terms of splicing dynamics / velocities.

jipeifeng commented 4 years ago

Thank you for the response! I'll have a try!