DOI: 10.5281/zenodo.17087021
title: Systematic review and mega-analysis of the peripheral blood transcriptome in depression implicates dysregulation of lymphoid cells and histones

description: This deposition accompanies Erady et al. 2025 and includes:

- Genome wide mega-analytic results for differential gene expression (DGE) and differential transcript expression (DTE), both sex-pooled and sex-stratified.

- Per-dataset differential transcript usage (DTU) results for RNAseq datasets (BIODEP, Le, Mostafavi datasets)

- Harmonised processed individual level count data, cell counts and metadata for datasets with permission for public sharing (HitDiP, Le, BIODEP - see below).

 

1) For files of the format xxx_counts_xxx.tsv:

   Row names correspond to Ensembl gene IDs and column names correspond to sample IDs

   Raw gene counts are provided

 

2) For files of the format xxx_metadata.tsv:

   Row names correspond to sample IDs

 

3) For files of the format DGE_MDD_CNT_xxx.tsv

   Gene names and Ensembl gene IDs are provided. Additional columns correspond to:



BacWeightedZ_meta: bias and inflation corrected, and meta-analysed Z-score

pvalue.pval_BacWeightedZ: p-value or significance of meta-analysed Z-score

pvalue.BacWeightedZ_adj_pval: p-value after Benjamini-Hochberg correction

EmpiricalEstimatedMean: bias calculated using the R package bacon

EmpiricalEstimatedSD: inflation calculated using the R package bacon


 

4) For files of the format DTE_MDD_CNT_xxx.tsv

   Gene names and Ensembl transcript IDs are provided. Additional columns correspond to:



BacWeightedZ_meta: bias and inflation corrected, and meta-analysed Z-score

pvalue.pval_BacWeightedZ: p-value or significance of meta-analysed Z-score

pvalue.BacWeightedZ_adj_pval: Benjamini-Hochberg adjusted meta-analytic p-values

EmpiricalEstimatedMean: bias calculated using the R package bacon

EmpiricalEstimatedSD: inflation calculated using the R package bacon


 

5) For files of the format DTU_MDD_CNT_cell_corrected_xxx.tsv

   Gene names, Ensembl gene IDs and Ensembl transcript IDs are provided. Additional columns correspond to:



p_transcript: per-transcript p-value as generated by DEXSeq

q_gene: per-gene adjusted p-value - evidence from multiple tests within a gene are aggregated into a single p-value and then FDR corrected for multiple testing across all genes

p_transcript_confirmation: stage-wise adjusted p-values - transcript-level p-values corrected for overall FDR using stageR. If the gene-level q-value (q_gene) is >0.05 or the gene has only one transcript, adjusted transcript p-values are not calculated


6) Per_dataset_pooled_DGE_cell_corrected_results.xlsx; full per-dataset summary statistics as input to the main meta-analysis (see Github for workflow). Results are per limma output; column 'B' indicates log-odds of differential expression.

 

7) Leave_one_out_DGE_meta_analysis_cell_corrected_pooled.xlsx; summary statistics for the 4 leave-one-out meta-analyses; column names are as per 3) above

 

NB. Individual-level count data are also available for the BIODEP dataset, but cannot be deposited publicly according to study ethics - please contact the authors for access; the data are available to all research groups (university email address required). The BIODEP data are available in the same format as detailed above.