PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimary200OK2000ProteomicsChristian von Mering3847https://pax-db.org/dataset/3847/7785906mering@imls.uzh.chUniversity of ZurichPAXDBFor the rescaling, the datasets are first parsed or processed such that the data reflect proportional abundances of whole protein molecules (i.e. proportionality to counts of complete, individual protein molecules, not to molecular weights, protein volumes, or digested peptides). In the case of spectral counting data protein. The proportional abundances are rescaled linearly to add up to one million; this means the abundance of each protein of interest is finally expressed in (parts per million,) relative to all other proteins in a sample. For a given protein abundance dataset, we then compute the absolute log abundance ratios of all pairs of proteins annotated to be functionally linked. The median of these absolute log abundance ratios represents an indirect quality metric: the closer it is to zero, the better (i.e. the more there is consistency between abundance values and functional annotations such as protein complexes or pathways). We then compute a background expectation for this metric, by permuting the abundance values in a given dataset randomly, and recomputing the median log abundance ratios. The permutation is repeated several times, yielding a distribution of medians. The actually observed median is then expressed as a Z-score distance to the random distribution ofmedians—this distance is termed the interaction consistency score.Plants are foundational for global ecological and economic systems, but most plant proteins remain uncharacterized. Protein interaction networks often suggest protein functions and open new avenues to characterize genes and proteins. We therefore systematically determined protein complexes from 13 plant species of scientific and agricultural importance, greatly expanding the known repertoire of stable protein complexes in plants. By using co-fractionation mass spectrometry, we recovered known complexes, confirmed complexes predicted to occur in plants, and identified previously unknown interactions conserved over 1.1 billion years of green plant evolution. Several novel complexes are involved in vernalization and pathogen defense, traits critical for agriculture. We also observed plant analogs of animal complexes with distinct molecular assemblies, including a megadalton-scale tRNA multi-synthetase complex. The resulting map offers a cross-species view of conserved, stable protein assemblies shared across plant cells and provides a mechanistic, biochemical framework for interpreting plant genetics and mutant phenotypes.A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies.McWhite Claire D CD, Papoulas Ophelia O, Drew Kevin K, Cox Rachael M RM, June Viviana V, Dong Oliver Xiaoou OX, Kwon Taejoon T, Wan Cuihong C, Salmi Mari L ML, Roux Stanley J SJ, Browning Karen S KS, Chen Z Jeffrey ZJ, Ronald Pamela C PC, Marcotte Edward M EMAdd, DmelCG43443, ADD, ADD-87, Hts-RC, data, AU023367, Data Set, protein complex, supply, Proteins, Ovhts, Gene, HtsRC, CG9325, protein, neutral molecular compounds, protein-containing complex, Dmel_CG9325, Xt, Peptide, 1B1, add, Polypeptides, anon-EST:Posey9, protein polypeptide chains, native protein, peptido, htsRC, GLI3-190, natural protein, polypeptide chain, Add-hts, Protein, CG43443, Gene Products, l(2)k14523, Dmel_CG34197, l(2)00634, median, Ovhts-RC, background, supply and distribution, protein aggregate, all_pairs, molecule, Bph, molecula, Random selection by shearing, oligonucleotide random primer, proportion, HTS-R1, HTS, Hts, molecules, peptides, l(2)k06121, adducin, GLI3FL, distribution, AI854843, proportionality, add-like, HTS-RC, rate, proteins, Molekuel, Pdn, sample population, introduction, Protein Gene Products, Gene Proteins, Adducin, RANDOM, 10^[-6], ppm, sample, supply., quotient, Peptid, peptidos, Polypeptide, Attention Deficit Hyperactivity Disorder, l(2)01103, EST D, CG34197, HtsF, ratioRABGAP5., Plant Protein, CG34403, l(4)13, Polyarteritis Nodosa, MUTYH-Associated Polyposis, methionine aminopeptidase activity, Periarteritis Nodosa, LEF/TCF-1, Dmel_CG17964, Proteins, MYH-associated polyposis, autosomal recessive familial adenomatous polyposis, Maps, DmelCG34403, IA5, LEF/TCF, LEF-1, Dm Pan, Dmel_CG32005, pan.dTCF, PERIANTHIA, Protein, LEF1/TCF, Classic Polyarteritis Nodosa, 2, Tcf, TCF, Tcf/LEF, familial adenomatous polyposis, MAP, peptidase M activity, autosomal recessive, Lef1, adenomas, periarteritis, RUTBC3, rabGAPLP, TCF/LEF, L-methionine aminopeptidase activity, LEF1, F24J5.12, familial adenomatous polyposis 2, Classical Polyarteritis Nodosa, Panarteritis Nodosa, Plant, DTCF, DTcf, RabGAP-5, Tcf-1, tcf, CG17964, d-TCF, MYH-Associated Polyposis, cTCF, l(4)102ABb, CG32005, F24J5_12, autosomal recessive multiple colorectal adenomas, RUSC3, Lef, TCF/LEF1, multiple colorectal, chimpanzees, MAP syndrome, lef1, polyarteritis, Pan, PAN, dTCF, dTcf, FAP2, colorectal adenomatous polyposisbud, adventitious bud (narrow), primordia, rudiment., future organ, placodeAgronomies, scale tissue, Materials, multi-cellular organism, methionine aminopeptidase activity, FESTA-L, FESTA-S, Pflanze, peltate hair, EG:163A10.2, Gene, Synthetases, Agronomy, Network, protein, Spectrum Analyses, Development, protein-containing complex, Interaction Network, Protein-Protein Interaction Network, viridiplantae, Transfer RNA, Protein Interaction Networks, protein polypeptide chains, Green Plants, Tier, polypeptide chain, Plants, heredity, Gene Products, Mass, 2, Vernalisation, AW048865, Analysis, l(1)3Cb, Animal, protein aggregate, Transfer, animal, Suppressor Transfer, notch, U19, familial adenomatous polyposis, Map, Mass Spectroscopy, MAP, peptidase M activity, Protein-Protein, Protein Interaction Map, l(1)Ax, Farming, plantae, Mass Spectrum Analysis, Animalia, adenomas, rabGAPLP, BM040, L-methionine aminopeptidase activity, Genetic, Analyses, plant peltate hair, familial adenomatous polyposis 2, DmelCG3936, RabGAP-5, plants, proteins, metazoa, dNotch, Ax, autosomal recessive multiple colorectal adenomas, Ligase, Devernalisation, RUSC3, co, Protein-Protein Interaction Map, species, Seed Stratification, NICD, NECD, EG:140G11.1, CT13012, Interaction Map, l(1)N, swb, Plant Protein, 16-178, Protein Interaction Network, 16-55, RNA, MUTYH-Associated Polyposis, Chp, protein complex, Co, body, Traits, animalia, land plants, Proteins, MYH-associated polyposis, Phenotypes., autosomal recessive familial adenomatous polyposis, Maps, whole body, anon-EST:Liang-1.12, Cistrons, Spectrum Analysis, Cell, predicted, Protein-Protein Interaction Maps, Spectroscopy, organism, tRNA, transfer ribonucleic acid, MS, native protein, natural protein, Protein, spl, shd, Metazoa, Thermomorphogenesis, Synthetase, Genetic Materials, transfer, 1.1, Ribonucleic acids, nd, Seed, scales, fa, Genetic Material, Mass Spectrum Analyses, autosomal recessive, Mass Spectrum, RUTBC3, whole organism, scale, Devernalization, Plant Cell, Plant, Spectrometry, Green Plant, Suppressor, MYH-Associated Polyposis, Stratification, TRAITS, RABGAP5, Protein Gene Products, Gene Proteins, higher plants, Protein Interaction, Protein-Protein Interaction, Agricultural, clone 1.12, Material, Protein Protein Interaction Map, Festa, Protein Protein Interaction Network, Koerper, multiple colorectal, Cells, Cistron, MAP syndrome, transfer RNA, CG3936, Protein-Protein Interaction Networks, n[fah], FAP2, Green, Agricultural Development, Suppressor Transfer RNA, colorectal adenomatous polyposis2falseGmax - Bud, SC (Mcwhiteetal.,cell2020)abundance based on Spectral counting, Interaction consistency score: 32.1, Coverage: 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