Plot genes with similar expression patterns
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ecg1g15 ▴ 30
@ecg1g15-19970
Last seen 4.1 years ago

Hi,

I have been using the "Analyzing RNA-seq data with DESeq2" (Love, Anders and Huber) and worked really well so far, thanks guys!

However, I would like to export and plot the different expression patterns of genes within my dataset. What I mean is to be able to group them by similar expression patterns +/- X error and see expression similarities responding to the conditions, and have different expression "trends" within the transcriptome.

I was wondering if there would be any function on DESeq2 or any other package that could do something similar? It would be interesting!

Cheers,

deseq2 R RNASeq • 1.8k views
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why not trying to cluster them based on their expression (heatmap, kmeans, SOM etc.) and than plot the separate groups. DESeq(2) was not meant for such results.

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@mikelove
Last seen 1 day ago
United States

I would start by computing the VST:

vsd <- vst(dds)

And then you can perform hierarchical clustering after computing Euclidean distance between genes. You can remove the row mean from each row, so that the baseline expression doesn't factor in.
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Thanks Michael, I have done many types of clustering using vsd. But more than doing a hierarchical clustering, I mean to plot the actual expression profiles (y-axis) over time/geography (x-axis), and then generate the cluster plots by profile similarity. (ie Cluster 1: gene expression gradual increase, cluster 2: gradual decrease; 3, peak in the middle, etc)

I have found the package "Mfuzz" from Bioconductor that apparently is available to work with RNASeq. Have you heard of it? Do you recommend any other?

Cheers

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Go for it. I have made these plots manually one time using base R: hclust, dist, rowMeans, lines, etc., but we don't have example code for this in the vignette.

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Thanks Michael, I have done many types of clustering using vsd. But more than doing a hierarchical clustering, I mean to plot the actual expression profiles (y-axis) over time/geography (x-axis), and then generate the cluster plots by profile similarity. (ie Cluster 1: gene expression gradual increase, cluster 2: gradual decrease; 3, peak in the middle, etc)

I have found the package "Mfuzz" from Bioconductor that apparently is available to work with RNASeq. Have you heard of it? Do you recommend any other?

Cheers

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I think the maSigPro package would be the one that you are looking for. I hope this helps.

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