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to all our speakers, just a friendly reminder, the time for each talk is 22 minutes, please keep your presentation within 20 minutes and leave 2 minutes for a quick question, thank you very much!
How does RECODE differ from conventional feature extraction using SVD?
What is the RNA-seq data projected on? That is, is there a physiological definition of the axis/surface onto which the projection is made?
In obtaining the v-mapper graph, how do you decide upon the nodes of the graph?
Is it possible to incorporate time series single cell RNAseq data in your method?
Hi, thanks for a very interesting talk! It is well known that gene expression can be limited by epigenetics factors. How does your method deal with that?
Wow, that’s a huge group!
Which software do use to obtain RNA velocity, velocyte or scVelo?
Like the v-mapper, is it possible to obtain gene regulatory relations (maybe by taking a transposed sc-RNAseq data)?
Thanks! Great presentation.
Jae Kyoung Kim
When P_i,j ^k is calculated, how AG_u and AN_j are determined?
How does this framework take into account the spatial distribution of different cell types and spread of ligands in space?
This is very exciting work! Are you only considering your work under normal conditions only? TGFbeta pathway involving macrophages and fibroblast is known to be altered in metastatic prostate cancer, so it could be really interesting application of your method!
Following Weitao’s question, what is the effect of competitions between receptors or signaling pathways in the framework?
Great talk, Jinsuo! Congratulations!
[Answer]TO Hari---What is the RNA-seq data projected on? That is, is there a physiological definition of the axis/surface onto which the projection is made?Since the Mapper result is represented by a graph structure, the axes/surfaces are undefinable for the projected graph.Mapper graph represents the closeness structure of cells.---In obtaining the v-mapper graph, how do you decide upon the nodes of the graph?Nodes are created by the same procedure as those of Mapper. V-Mapper only determines the direction of the Mapper graph.
---Like the v-mapper, is it possible to obtain gene regulatory relations (maybe by taking a transposed sc-RNAseq data)?By applying the method to gene-cell data instead of cell-gene data (transposed matrix), we can obtain a gene (gene cluster) network. However, since Mapper edge represents the closeness of clusters, the edges may NOT correspond to the regulations.Now we have also developed the gene regulatory network estimation method from scRNA-seq data by using another statistical approach.
TO Chen---Is it possible to incorporate time series single cell RNAseq data in your method?Yes. But we have to note that the gap or batch effects of time series data.
TO Tyczynska---Hi, thanks for a very interesting talk! It is well known that gene expression can be limited by epigenetics factors. How does your method deal with that?Yes, it is true. We now use the only transcriptome. We plan to combine transcription and epigenetic data using the noise reduction technique.
TO Muto--- Which software do use to obtain RNA velocity, velocyte or scVelo?I used scVelo. Both codes are applicable (we used stady-state algorithm).
Thank you very much!
Thank you, Yusuke. Great talk!
Thank you for your questions!
@weitao In this work, we did not consider the spatial effect. But we are working on it now, which is definitely a very important factor.
Thank you. Will follow your future work!
@Gosia, our approach can be applied to any single cell datasets across different conditions.
Thank you Yusuke! Has the work been published? And do you have a publicly available tool that implements your method?
@Jia, the competitions between receptors and signaling pathways is important and complicated. In this work, we did not consider such case. But will be very interesting to study it in the future.
Thank you Suoqin! Very nice talk
Thank you! That’s great! I’m just saying that it could be really interesting to apply your method to quantify the differences in cell-to-cell signaling in cancer compared to normal cells.
@Hari Thank you for your constructive comments. Sorry, we are writing the paper and preparing this code. If you test Mapper, I think a public code k-Mapper (https://kepler-mapper.scikit-tda.org/) is useful.
Thank you for the link Yusuke! I was actually more interested in testing out the denoising part of your method. It can have immediate applications in my work. Looking forward to your paper!
Hi Dae Wook! Great talk! :) As you know, there are a lot of cells and tissues. Which cells did you test?
Dear all, could you find the fourth speaker Chansoo Kim? I didn’t see Chansoo Kim in the current zoom meeting.
Hello, I'm Haneol Cho in Korea Iinstitute of Science and Technology and I'll present about KMC model behalf of Chansoo Kim
Thank you very much!