Genomics & Multi-omics Integration
How to integrate RNA-seq and proteomics data for a systems-level view of gene regulation.
Why Integrate Transcriptomics and Proteomics?
mRNA abundance does not always predict protein abundance. Post-transcriptional regulation, translation efficiency, and protein turnover create substantial divergence between the two layers. Joint analysis reveals regulatory mechanisms from transcription factor activity to protein degradation that neither layer alone can uncover.
Our Integration Workflow
Data Preprocessing & Normalisation
Combat/limma for RNA-seq, median ratio or VSN for proteomics. Batch correction using Harmony or limma::removeBatchEffect.
Correlation Analysis
Gene-level Spearman correlation, mRNA-protein concordance plots, and identification of discordant gene sets for regulatory analysis.
Pathway & Network Integration
Over-representation and GSEA on both layers, followed by integrative network construction using weighted gene co-expression network analysis (WGCNA) or DIABLO.