Supplementary Files 1& 2: Thompson & Pickard: The amino acid composition of a protein influences its expression

Supplementary File 1 - Dataset in Excel spreadsheet form associated with paper submitted to PLOS ONE TAB, TITLE, Description 1 Amino acid composition calculator The Excel methodology for extracting amino acid frequency data from each individual protein in a proteome downloaded in FASTA format 2 Human proteome AA composition Summary Table of amino acid composition for each protein in the human proteome. Additional characteristics are also included such as AA analysis by nutritional class. 3 25 selenocysteine The 25 human proteins that contain a selenocysteine substitution which make the CHECKSUM of the analysis of all 20 conventional analysis deviate from a total of 1 4 Testing pop. norm. distribution Lilliefors/Kolmogorov-Smirnov Tests of fEAA and fCEAA distritbution profiles 5 Relative proportions of E, C, N Methodology for creating smoothed plots of realtive proprtions of nutritional class of amino acids as a function of expression rank. 6 MLR Multiple Linear Regression analyses between amino acid frequency/property and expression level - across human organs, species. Summary tables for each test are shown together with the summary table 7 High fEAA & fCEAA diseases Those proteins at the extremes of AA composition with multiple DisGeNET disease annotations 8 Multigenic disease statistics Lists of manually collated or published disease risk proteins for several diseases/phenotypes. Statistical analysis of their fAA profiles compared to the whole proteome distribution. Supplementary File 2 - Dataset in Excel of Gene Ontology analyses: plotting the MLR+ and MLR- values for each protein in that gene ontology group. Asking whether each MLR distribution (+/-) significantly differs from the entire population distribution of proteins in the proteome. TAB TITLE 1 E. coli abiotic stress 2 E. coli translation 3 S. cerevisiae translation 4 A. thaliana translational elongation 5 A. thaliana high light intensity 6 A. thaliana water deprivation 7 A. thaliana cold acclimation 8 H. sapiens detoxification 9 H. sapiens cytoplasmic translation 10 H. sapiens response to stress