Table 1 Summary of analytical methods in the context of the conceptual framework (predisposition, onset, illness) with examples of data sources and studies for which these methods are employed.

From: Integrating genetics and transcriptomics to study major depressive disorder: a conceptual framework, bioinformatic approaches, and recent findings

Perspective

Data source

Analytical method

Examples

Predisposition

Human genotype

GWAS

[3, 4]

Human GWAS summary data and postmortem-brain-derived QTLs

Colocalization

[158]

 

Mendelian randomization

[3]

 

Transcriptomic imputation

[20, 158, 164, 218]

 

Drug repurposing analyses

[3, 20, 162]

hiPSC-derived brain cell transcriptomic data

Gene set enrichment

[59, 60, 169]

Onset

Mouse genotype and brain transcriptomic data

Context-specific QTL analysis

[178]

Human genotype and transcriptomic data

Context-specific QTL analysis

[64, 179, 180]

hiPSC-derived cells + glucocorticoids

Context-specific QTL analysis

[58]

 

Gene set enrichment

[58, 181, 182]

Mouse brain transcriptomic data + stress

Gene set enrichment

[61, 62, 183, 184]

 

Co-expression networks

[61, 183]

Illness

Human postmortem brain single cell/nuclei RNA-seq

Gene set enrichment

[207]

 

Co-expression networks

[207]

 

Cell type deconvolution

[207]

Human postmortem brain transcriptome

Gene set enrichment

[6, 7, 208]

 

Co-expression networks

[6, 7]

 

Cell type deconvolution

[208]

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