expression: patterns of expression across tissues

[stephens999]

Here the idea is to do analogues of the previous issues, but based on raw expression, not eQTLs. Kushal has already done a bunch of this - eg the structure analysis and clustering of tissues he presented at last gtex meeting. It just needs putting in one place here.

• heatmap showing pairwise similarity of tissues in terms of expression.
• tsne clustering of tissues showing similar patterns of expression.
• structure analysis, clustering tissues. (tsne clustering of structure results?)
• sfa of expression data?

[kkdey]

Subissues 2,3:

The tsne clustering of tissues (without and with structure) is in this link: https://github.com/stephens999/gtex-viz/blob/master/gtex.Kushal/plots/tissues_tSNE.html

Subissue 4:

Will it better to do a Shiny plot for the 15 factors in tissue SFA??

[kkdey]

Did a shiny RmD file for easier viewing of the factors.... the link: https://github.com/stephens999/gtex-viz/blob/master/gtex.Kushal/src/sfa.genes.shiny.Rmd

[kkdey]

Addresses subissue 4

[kkdey]

The intra class correlation plot of the individuals across tissues...distinctly shows correlation across the brain sub tissues, addresses subissue 1 : https://github.com/stephens999/gtex-viz/blob/master/gtex.Kushal/plots/brain_ICC.html

I did not add the .Rmd file because it has input data files bigger than 200 mb which I could not upload on Github....

[kkdey]

I now have a scatter plot for a gene (the most highly expressed gene) for Brain Amygdala and Brain Hypothalamus : https://github.com/stephens999/gtex-viz/blob/master/gtex.Kushal/plots/brain_scatter_plot.pdf

Also for the same gene between Skin exposed and not exposed : https://github.com/stephens999/gtex-viz/blob/master/gtex.Kushal/plots/skin_scatter_plot.pdf

And a heatmap of the proportion of cases having correlation more than 0.3 across tissues (brain tissues clearly show higher proportion) : https://github.com/stephens999/gtex-viz/blob/master/gtex.Kushal/plots/cor_thresh_0_3.pdf

[kkdey]

I have the matrix of proportion values now on Github: https://github.com/stephens999/gtex-viz/blob/master/gtex.Kushal/data/prop_sig_matrix_0_3.txt

You can just read it and form the heatmap and it should show same patterns as in cor_thresh_0_3