AMP PD Transcriptomics Differential Expression All Time Points

Note: The analysis that produced this target list is available to all registered AMP PD users in Terra and can be reused in your work.

Introduction

The AMP-PD Target Explorer uses transcriptomic data described here.

3 Studies were included in this analysis:

Methods:

Outliers and covariates

Outlier samples

• Principal components were correlated to metadata and QC metrics. RIN and PCT USABLE BASES (Picard RnaSeqMetrics) were used to set cut offs for outlier detection.
• Tools:
  • R

Covariates

• To help identify covariates, principal components were correlated to metadata and QC metrics. variancePartition was used to validate potential covariates. Finally a neutrophil score was developed to fill the gap in CBC data.
• Tools:
  • R
  • variancePartition
• Input:
  • fullTableRNAseqMeta_TNT.csv created by: Terra Notebook
  • neutAndLymph.csv generated using: Lymphocyte and neutrophil enriched genes, from Protein Atlas Human Proteome
• Output:
  • default covariates: sex + plate + age + neutPerc + lymphPerc

Expression

Differential expression

• Cohorts for DE were created by filtering metadata for case/control status, visit month, and genetic mutation status. DE was performed with and without neutrophil score as a covariate.
• Tools:
  • R
  • edgeR
  • limma
  • Transcriptomics Differential Expression Terra Workspace
• Input:
  • matrix.featureCounts.tsv - raw count data (output from Subread featureCounts)
  • fullTableRNAseqMeta_TNT.csv - table of relevant sample metadata
• Output:
  • _limmaResults.tsv - differential expression table including fold change, p-values, and average expression
  • Plots (volcano and mean difference)