{"database":"PAXDB","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["http://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Christian von Mering"],"species":["4081"],"full_dataset_link":["https://pax-db.org/dataset/4081/3494796433"],"submitter_email":["mering@imls.uzh.ch"],"submitter_affiliation":["University of Zurich"],"sample_protocol":[""],"repository":["PAXDB"],"data_protocol":["For the rescaling, the\ndatasets are first parsed or processed such that the data reflect\nproportional abundances of whole protein molecules\n(i.e. proportionality to counts of complete, individual protein\nmolecules, not to molecular weights, protein volumes, or digested\npeptides). In the case of spectral counting data protein. The proportional abundances are rescaled linearly to add up\nto one million; this means the abundance of each protein of\ninterest is finally expressed in (parts per million,) relative to\nall other proteins in a sample. \nFor a given protein abundance dataset, we then compute\nthe absolute log abundance ratios of all pairs of proteins\nannotated to be functionally linked. The median of these absolute\nlog abundance ratios represents an indirect quality\nmetric: the closer it is to zero, the better (i.e. the more there\nis consistency between abundance values and functional annotations\nsuch as protein complexes or pathways). We then\ncompute a background expectation for this metric, by permuting\nthe abundance values in a given dataset randomly,\nand recomputing the median log abundance ratios. The permutation\nis repeated several times, yielding a distribution of\nmedians. The actually observed median is then expressed as a\nZ-score distance to the random distribution ofmedians—this\ndistance is termed the interaction consistency score."],"pubmed_abstract":["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."],"pubmed_title":["A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies."],"pubmed_authors":["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 EM"],"data_synonyms":["Add, 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, ratio"],"pubmed_title_synonyms":["RABGAP5., 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 polyposis"],"name_synonyms":["Lycopersicon (Mill.) Seithe, exact)., exact), hoja (Spanish, 葉 (Japanese, Lycopersicum"],"pubmed_abstract_synonyms":["Agronomies, scale tissue, Materials, multi-cellular organism, methionine aminopeptidase activity, FESTA-L, FESTA-S, Pflanze, peltate hair, EG:163A10.2, Gene, Agronomy, protein, Spectrum Analyses, Development, protein-containing complex, viridiplantae, Transfer RNA, protein polypeptide chains, Tier, polypeptide chain, heredity, Gene Products, Mass, 2, Vernalisation, AW048865, Analysis, l(1)3Cb, Animal, protein aggregate, Transfer, animal, Suppressor Transfer, notch, U19, familial adenomatous polyposis, Mass Spectroscopy, MAP, peptidase M activity, 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, Devernalisation, RUSC3, co, species, Seed Stratification, NICD, NECD, EG:140G11.1, CT13012, l(1)N, swb, Plant Protein, 16-178, 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, Spectroscopy, organism, tRNA, transfer ribonucleic acid, MS, native protein, natural protein, Protein, spl, shd, Metazoa, Thermomorphogenesis, Genetic Materials, transfer, 1.1, Ribonucleic acids, nd, Seed, scales, fa, Genetic Material, Mass Spectrum Analyses, autosomal recessive, Mass Spectrum, RUTBC3, whole organism, distinct, scale, Devernalization, Plant Cell, Plant, Spectrometry, Suppressor, MYH-Associated Polyposis, Stratification, TRAITS, RABGAP5, Protein Gene Products, Gene Proteins, higher plants, Agricultural, clone 1.12, Material, Festa, Koerper, multiple colorectal, Cells, Cistron, MAP syndrome, transfer RNA, CG3936, n[fah], FAP2, Agricultural Development, Suppressor Transfer RNA, colorectal adenomatous polyposis"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"S.lycopersicum - Leaf, SC (Mcwhiteetal.,cell2020)","description":"abundance based on Spectral counting, Interaction consistency score: 5.0, Coverage: 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