Systematic reanalysis of co-fractionation mass spectrometry data: predicted interactomes

<p>This upload contains predicted interactomes for 27 species or clades: 17 individual organisms with at least three published CF-MS experiments, and 9 phylogenetic groupings of those organisms.&nbsp;</p> <p>The following individual organisms are represented:</p> <ul> <li>Arabidopsis thaliana</li> <li>Brassica oleracea</li> <li>Caenorhabditis elegans</li> <li>Chaetomium thermophilum</li> <li>Chlamydomonas reinhardtii</li> <li>Dictyostelium discoideum</li> <li>Drosophila melanogaster</li> <li>Nematostella vectensis</li> <li>Homo sapiens</li> <li>Mus musculus</li> <li>Oryza sativa</li> <li>Plasmodium berghei</li> <li>Plasmodium falciparum</li> <li>Plasmodium knowlesi</li> <li>Strongylocentrotus purpuratus</li> <li>Triticum aestivum</li> <li>Trypanosoma brucei</li> <li>Xenopus laevis</li> </ul> <p>The following clades are also represented:</p> <ul> <li>BOP clade</li> <li>Deuterostomia</li> <li>Eucharontoglires</li> <li>Eukaryota</li> <li>Mesangiospermae</li> <li>Opiskothonta</li> <li>Plasmodium</li> <li>Tetrapoda</li> <li>Viridaplantae</li> </ul> <p>The interactomes are provided in two forms. Files in the &#39;All interactions&#39; directory include the complete classifier scores for every possible protein pair (sorted in descending order). Files in the &#39;50% precision&#39; directory include only those interactions identified above 50% precision, for convenience.&nbsp;</p> <p>Proteins were mapped to orthogroups using eggNOG. Maps from eggNOG orthogroups to UniProt accessions are available from https://github.com/skinnider/CF-MS-analysis/tree/master/data/resources/eggNOG. The phylogenetic tree used to group species into clades is also available from https://github.com/skinnider/CF-MS-analysis/tree/master/data/resources/TimeTree/species.nwk.</p> <p>The third and final directory, &#39;Human&#39;, contains the consensus CF-MS human interactome, in which proteins were merged across 46 human experiments by their gene names, rather than based on eggNOG orthogroups. The directory contains both complete classifier scores (file &#39;classifier-scores.tsv.gz&#39;) and the consensus CF-MS interactome, at 50% precision (file &#39;CF-MS-interactome.tsv&#39;).</p>