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

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. 

The following individual organisms are represented:

Arabidopsis thaliana

Brassica oleracea

Caenorhabditis elegans

Chaetomium thermophilum

Chlamydomonas reinhardtii

Dictyostelium discoideum

Drosophila melanogaster

Nematostella vectensis

Homo sapiens

Mus musculus

Oryza sativa

Plasmodium berghei

Plasmodium falciparum

Plasmodium knowlesi

Strongylocentrotus purpuratus

Triticum aestivum

Trypanosoma brucei

Xenopus laevis

The following clades are also represented:

BOP clade

Deuterostomia

Eucharontoglires

Eukaryota

Mesangiospermae

Opiskothonta

Plasmodium

Tetrapoda

Viridaplantae

The interactomes are provided in two forms. Files in the 'All interactions' directory include the complete classifier scores for every possible protein pair (sorted in descending order). Files in the '50% precision' directory include only those interactions identified above 50% precision, for convenience. 

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.

The third and final directory, 'Human', 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 'classifier-scores.tsv.gz') and the consensus CF-MS interactome, at 50% precision (file 'CF-MS-interactome.tsv').