Identifying the genes impacted by cell proliferation in proteomics and transcriptomics studies
Fig 2
Signature genes of cell proliferation.
a-b) Definition of the cutoff for correlation with pseudo-proliferation index with three sets of gold standards in the proteomes (a) and the transcriptomes (b). Proteins/genes were ranked by decreasing absolute Pearson correlation to pseudo-proliferation index (horizontal axis) and the vertical axis presents the cumulative number of gold standards for each set. Proteins/genes quantified in less than 3 and 2 data sets were excluded in (a) and (b), respectively. c) Scatter plot of the mean Pearson correlation to pseudo-proliferation index at protein (vertical axis) and transcript (horizontal axis) level across all data sets. The red areas contain the proteins above the threshold in the proteome and/or transcriptome and the rectangle with white borders indicates the final list of proliferation signature genes defined in this study. The point distribution in the proteomes and transcriptomes are presented on the sides of the plot.