Question: Finding genes differently expressed in time series data
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14 days ago by
F3.0k wrote:


I have Control cell line day1 to day 26 and Lead(pb) treatment day1 to day26. The experimental design aims to get the impact of Lead(pb) on developmental process .I must look if there are group of developmental genes that cluster differently in the lead(pb) experiment. For instance some genes are differentially expressed directly or others are coming in later time points. First I thought about WGCNA (figure) in which I think genes in significant modules in days 1-3 make sense for me. Then I thought about SOM clustering but clusters don't show any up or down regulation in day points

Any help please?

rna-seq R gene • 131 views
ADD COMMENTlink written 14 days ago by F3.0k

It depends on which definition of cluster you're interested in. For time series, I would compute a distance matrix based on dynamic time warping (see for example the R package dtw, be sure to read the FAQ down the page) and use this matrix as input for a clustering algorithm.

ADD REPLYlink written 14 days ago by Jean-Karim Heriche14k

Thanks a lot, for example in picture A (cluster 28 with 103 genes), genes toward week 9 are being up regulated and in cluster 3 with 203 genes to the end of development down regulated.

ADD REPLYlink modified 14 days ago • written 14 days ago by F3.0k

What I had in mind was for you to compute a distance matrix using dtw for each condition separately then use this for simultaneous clustering using for example a tensor factorization method as I wrote in a recent answer which you've seen.

ADD REPLYlink written 14 days ago by Jean-Karim Heriche14k

Thanks a lot for sharing your idea. I have 52 samples (without replicates); control_day1 vs lead_day1 to control_day26 vs lead_day26. Then by dtw I must calculate 26 distance matrices for each control_day vs lead_day?????

Thanks again to help people to figure out

ADD REPLYlink written 13 days ago by F3.0k
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