STEP 4

Assessment of technical bias in complex correlations

Co-abundances of proteins were calculated as Pearson correlations between protein abundances across individuals. As a control proteins that were not part of any complex assembly were randomly assigned into artificial complexes and cross-correlated as well (Figure S2B). In addition, the data was also permuted and proteins subunits were again tested for co-abundance using Pearson correlation (Figure S2B). The Mann-Whitney U-test was applied to assess significance.

Data/Code Requirements for downloading

complex_filtered_battle_protein.tsv.gz (3MB)

complex-mapped and -filtered proteomics data from Battle et al. (2015), Science (Human Individuals)

complex_filtered_battle_ribo.tsv.gz (4.9MB)

complex-mapped and -filtered ribosome profiling data from Battle et al. (2015), Science (Human Individuals)

complex_filtered_battle_rna.tsv.gz (4.9MB)

complex-mapped and -filtered RNAseq data from Battle et al. (2015), Science (Human Individuals)

complex_filtered_gygi1.tsv.gz (2.2MB)

complex-mapped and -filtered proteomics data from Chick et al. (2016), Nature (Founder Mouse strains, MS-proteomics)

complex_filtered_gygi2.tsv.gz (3.9MB)

complex-mapped and -filtered RNAseq data from Chick et al. (2016), Nature (Founder Mouse strains, RNA-seq)

complex_filtered_gygi3.tsv.gz (2.8MB)

complex-mapped and -filtered proteomics data from Chick et al. (2016), Nature (Founder Mouse strains, MS-proteomics)

complex_filtered_mann.tsv.gz (3.7MB)

complex-mapped and -filtered proteomics data from Geiger et al.(2012), Mol Cell Proteomics (Human Cell Types)

complex_filtered_tcga_breast.tsv.gz (2.2MB)

complex-mapped and -filtered proteomics data from Mertins et al. (2016), Nature (TCGA Breast Cancer)

complex_filtered_tcga_color.tsv.gz (1.3MB)

complex-mapped and -filtered proteomics data from Roumeliotis et al. (2017),Cell (TCGA Colorectal Cancer)

complex_filtered_tcga_ovarian.tsv.gz (2.9MB)

complex-mapped and -filtered proteomics data from Zhang et al. (2016), Cellf (TCGA Ovarian Cancer)

Download all input data for this step here (31.7MB)

wp_step4_code.py

Python code required for reshuffling datasets, complexes and calculating correlation values.

underlying_data_for_suppFig2b.zip (1MB)

Underlying data for Supplementary Figure 2b

Supplementary Figure 2b