Data Analysis Modules: panoply_rna_protein_correlation

panoply_rna_protein_correlation

Description

Measures and plots correlation between mRNA expression and protein abundance for each gene-protein pair using pearson correlation. Protein IDs are mapped to gene symbols; PTM sites are rolled-up to the protein level before mapping to gene symbols. The module outputs correlation tables and histograms summarizing RNA-protein correlation. See (Zhang et al., 2014) and (Mertins et al., 2016).

Input

Required inputs:

• inputData: (.tar file) tarball from panoply_normalize_ms_data or normalized protein/PTM site data in gct format (when standalone is TRUE)
• rnaExpr: (.gct file) RNA expression data
• type: proteomics data type
• standalone: (String) set to TRUE to run as a self-contained module; if TRUE the analysisDir input is required
• yaml: (.yaml file) parameters in yaml format

Optional inputs:

• rnaSDthreshold: (Int, default = 1) for standard deviation variation filter; set to NA to disable
• profilePlotTopN: (Int, default = 25) plots showing RNA and protein levels across samples for the topN gene-protein pairs (sorted by correlation) are generated
• analysisDir: (String) name of analysis directory
• outFile: (String, default = "panoply_rna_protein_correlation-output.tar") output .tar file name

Output

• outputs: Tarball including the following files in the rna subdirectory:
  • Harmonized (rna-seq.gct) and filtered (rna-seq-sdfilter.gct) RNA data with sample order matching that in the proteome data table
  • Tables listing RNA-protein correlation for every gene-protein pair (*-mrna-cor.tsv) and the best gene-protein pairs with highest (correlation > 0.7), statistically significant correlation (*-mrna-cor-best.tsv)
  • Plots showing histograms of RNA-protein correlation for the following gene-protein pairs:
    • all gene-protein pairs (*-mrna-cor.pdf)
    • best pairs (*-mrna-cor-best.pdf)
    • statistically significant pairs (*-mrna-cor-sig.pdf)
    • all pairs, with statistically significant pairs highlighted (*-mrna-cor-combined.pdf)
    • plots showing RNA and protein levels across samples for the topN gene-protein pairs

References

• Zhang, B., Wang, J., XiaojingWang, Zhu, J., Liu, Q., Shi, Z., Chambers, M., Zimmerman, L., Shaddox, K., Kim, S.,et al. (2014). Proteogenomic characterization of human colon and rectal cancer. Nature https://dx.doi.org/10.1038/nature13438
• Mertins, P., Mani, D., Ruggles, K., Gillette, M., Clauser, K., Wang, P., Wang, X., Qiao, J., Cao, S., Petralia, F., et al. (2016). Proteogenomics connects somatic mutations to signalling in breast cancer. Nature 534(7605), 55 - 62. https://dx.doi.org/10.1038/nature18003.