Fig. 6: Functionally related peptides were connected in peptide abundance correlation networks for species representative genomes constructed with SCCs of TNPA log2-FC of individual V52.

A Correlation between SCCs of peptide log2-FC based on TNPA and SCCs based on OPA (original peptide abundance) in the top ten genomes from individual V52. B, C Higher modularity and lower clustering coefficient of peptide correlation networks constructed with SCC of TNPA log2-FC than networks constructed with SCC of OPA log2-FC. D Comparison of representative peptide correlation networks for species representative genomes constructed with TNPA and OPA. Nodes are colored according to their modularity class from Gephi. E Proportion of peptide pairs from the same protein in peptide correlation networks for species representative genomes compared to the proportion in all peptide pairs from the corresponding species representative genome. F Proportion of peptide pairs from proteins potentially located near each other in the genome (\(\le\)10 gene ID difference) in peptide correlation networks for species representative genomes compared to the proportion in all peptide pairs from the corresponding species representative genomes. ** indicates statistical significance at the p \(\le\) 0.01 level by two-sided Mann–Whitney U-test. G, H Peptide abundance correlation networks for species representative genomes MGYG000004769 and MGYG000002528. Peptides from proteins with only one peptide in the network were removed. Peptides from the top eight proteins with the most peptides in each network are annotated with distinct colors, and peptides from other proteins are colored gray.