DEG_LDSC

Authors: Alice Yu and Hyejung Won

Created: 7/11/2021

Updated: 7/20/2021

Each folder contains Stratified LD Score Regression (S-LDSC) annotation file for each transcriptomic feature.

Each folder contains two subdirectories:

• Hi-C: annotation file generated based on Hi-C evidence
• QTL: annotation file generated based on QTL evidence

Cell-type specific DEG

• Reference: Ruzicka, W.B. et al.(2020) medRxiv doi: https://doi.org/10.1101/2020.11.06.20225342

DEG/DET

• Reference: Gandal, M.J. et al.(2018) PMID: 30545856
• Differentially expressed genes (DEGs) or differentially expressed transcriptions (DETs) with FDR < 0.05 were stratified into up- and downregulated genes based on log2 fold change (logFC)

Gene Co-expression Modules

• PsychENCODE Consortium (PEC): Gandal, M.J. et al.(2018) PMID: 30545856
• CommonMind consortium (CMC): Fromer, M. et al.(2016) PMID: 27668389

Isoform-level Co-expression Modules

• Reference: Gandal, M.J. et al.(2018) PMID: 30545856

kME/kTotal

• kME (PEC): Gandal, M.J. et al.(2018) PMID: 30545856
• kTotal (CMC): Fromer, M. et al.(2016) PMID: 27668389
• Genes classified into 10 groups based on centrality/connectivity values

Transcription Factor-Target Gene

• Reference: Wang, D. et al.(2018) PMID: 30545857

fishers_TF-Target_genes.R

• Script runs Fisher's Exact Test with protein-coding DEGs and target genes of schizophrenia-associated transcription factors (TFs)
• Schizophrenia-associated TFs were defined using TFs of high-confidence schizophrenia risk genes from PEC

.results

• Contains heritability enrichment and significance of each transcriptomic feature
• Cols
  • Prop._SNPs: Proportion of SNPs
  • Prop._h2: Proportion of heritability
  • Prop._h2_std_error: Standard Error of heritability
  • Enrichment: Heritability Enrichment
  • Enrichment_std_error: Standard Error of Heritability Enrichment
  • Enrichment_p: P-value of enrichment

Functional Genomic Data

• Hi-C, eQTL, and isoQTL: Wang, D. et al.(2018) PMID: 30545857
  • Used data generated from dorsolateral prefrontal cortex (DLPFC)

Reference

Please cite this paper: Yu, A.W.; Peery, J.D.; Won, H. Limited Association between Schizophrenia Genetic Risk Factors and Transcriptomic Features. Genes 2021, 12, 1062. https://doi.org/10.3390/genes12071062

SCZ GWAS: Pardinas, A.F. et al.(2018) PMID: 29483656

S-LDSC (v1.0.1): Finucane, H.K. et al.(2015) PMID: 26414678

• Baseline model (v1.1.0) was used to assess heritability enrichment

H-MAGMA input file: Sey, N.Y.A. et al.(2020) PMID: 32152537

• Used to identify SNPs mapped to each gene