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.

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

Data embargo until 01/12/2023
Date made available2 Oct 2023
PublisherUniversity of Strathclyde

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