Differential expression at gene level widget

[kdaily]

A forest plot of effect estimates for set of genes as a fxn of brain region/disease?

[kdaily]

volcano plot, per brain region/study?

[kdaily]

table/summary of expression levels as fxn of disease status

[kdaily]

Using these datasets of summary statistics:

• syn8468023 (mayo)
• syn10157628 (msbb)
• syn8456721 (rosmap)

[kdaily]

Unsure about what set of columns is required for uniqueness, looks like:

Model, Comparison, BrainRegion.ref, BrainRegion.ag, Gender.ref, Gender.ag, AOD.ref, AOD.ag, ensembl_gene_id, hgnc_symbol, logFC, CI.L, CI.R, AveExpr, adj.P.Val

But MSBB and ROSMAP do not have BrainRegion.ref and BrainRegion.ag columns.

[blogsdon]

@th1vairam is the person to answer this question

[th1vairam]

Here is a merged table from all three studies, 4 models with 7 brain regions and 4 comparisons https://www.synapse.org/#!Synapse:syn11180450

[th1vairam]

This is the code I used to do the above merge https://github.com/th1vairam/Brain_Reg_Net/blob/AMPAD_reprocessing/code/R/collateDifferentialExpressionResults.R

[kdaily]

Done.