{"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":["4932"],"full_dataset_link":["https://pax-db.org/dataset/4932/527300760"],"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":["Uncovering the mechanisms underlying robust responses of cells to stress is crucial for our understanding of cellular physiology. Indeed, vast amounts of data have been collected on transcriptional responses in Saccharomyces cerevisiae. However, only a handful of pioneering studies describe the dynamics of proteins in response to external stimuli, despite the fact that regulation of protein levels and localization is an essential part of such responses. Here we characterized unprecedented proteome plasticity by systematically tracking the localization and abundance of 5,330 yeast proteins at single-cell resolution under three different stress conditions (DTT, H2O2, and nitrogen starvation) using the GFP-tagged yeast library. We uncovered a unique \"fingerprint\" of changes for each stress and elucidated a new response arsenal for adapting to radical environments. These include bet-hedging strategies, organelle rearrangement, and redistribution of protein localizations. All data are available for download through our online database, LOQATE (localization and quantitation atlas of yeast proteome)."],"pubmed_title":["A novel single-cell screening platform reveals proteome plasticity during yeast stress responses."],"pubmed_authors":["Breker Michal M, Gymrek Melissa M, Schuldiner Maya M"],"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":["screening, dTAF[[II]]230, TAF[[II]]250, d230, findings, lager beer yeast., TAF200, total expressed protein, l(3)84Ab, baker's yeast, dTAFII250, BG:DS00004.13, TAFII-250, TAF250/230, EfW1, Cell, Saccharomyces italicus, Saccaromyces cerevisiae, dTAF230, dmTAF[[II]]230, Sccharomyces cerevisiae, TAFII250, Screenings, dmTAF1, Taf230, Mass Screenings, p230, yeast, symptoms, Mass, TAF[[II]]250/230, Screening, TFIID, TAF250, Saccharomyces oviformis, Taf[[II]]250, Yeast, Taf200, dTAF[[II]]250, TAF[[II]]230, TFIID TAF250, cel, cell, signs, Saccharomyes cerevisiae, Taf1p, TAF[II]250, CG17603, Saccharomyces uvarum var. melibiosus, TAF[[II]], dTAF250, DmelCG17603, Candida robusta, Taf250, Saccharomyces capensis, SR3-5, brewer's yeast, TAF, Proteomes, TAF230, TAF1"],"name_synonyms":["Taf[[II]]250, Taf200, dTAF[[II]]230, TAF[[II]]250, d230, multi-cellular organism, dTAF[[II]]250, TAF[[II]]230, whole organism, TFIID TAF250, cel, body, cell, TAF200, l(3)84Ab, whole body, dTAFII250, Taf1p, TAF[II]250, BG:DS00004.13, TAFII-250, CG17603, TAF250/230, TAF[[II]], EfW1, Cell, dTAF230, dTAF250, dmTAF[[II]]230, organism, TAFII250, DmelCG17603, TAF1., Taf250, dmTAF1, SR3-5, Taf230, p230, Koerper, TAF[[II]]250/230, TFIID, TAF, animal, TAF230, TAF250"],"pubmed_abstract_synonyms":["Bret, Regulations, HOOH, protein levels, Plantar Prints, d230, rac-Dithiothreitol, Plantar Print, 1-carboxy-N, threo-1, H2O2, DEP-1, Cleland's reagent, Print, Brewer's, Oxydol, baker's yeast, Gene, dTAFII250, AI450271, Scc-1, protein, Organelle, protein-containing complex, EfW1, dihydrogen dioxide, Saccharomyces italicus, Social Controls, dmTAF[[II]]230, Readability, protein polypeptide chains, polypeptide chain, dmTAF1, Taf230, responsivity, yeast, Gene Products, establishment and maintenance of position, (trimethylammoniumyl)acetate, establishment and maintenance of substrate location, protein aggregate, Formal Social Controls, lager beer yeast, abromine, TAF250, trimethylglycine, (R*, Ptpb2, FACT80, reactivity, Taf200, perhydrol, Fingerprints, dTAF[[II]]250, TFIID TAF250, cel, FACT, cell, N, C1, Saccharomyes cerevisiae, Taf1p, Baker, proteins, Saccharomyces uvarum var. melibiosus, S. cerevisiae, Social, Trimethylammonioacetate, dTAF250, S cerevisiae, Candida robusta, Saccharomyces capensis, Trimethylaminoacetate, [OH(OH)], BET, Bet, acidol, Baker's, 2-N, Mycoderma cerevisiae, Plantar, 1883, brewer's yeast, TAF, Prints, 3-butanediol, establishment and maintenance of substance location, data, dTAF[[II]]230, TAF[[II]]250, N-Trimethylglycine, Saccharomyces cerevisiae 'var. diastaticus', Formal Social Control, protein complex, UNQ262/PRO299, Proteins, bet, TAF200, total expressed protein, l(3)84Ab, Betaine, function, BG:DS00004.13, 4-dimercapto-2, TAFII-250, TAF250/230, Cell, Saccaromyces cerevisiae, Dithiothreitol, dTAF230, Dithiotreitol, Baker's Yeasts, Sccharomyces cerevisiae, Fingerprint, single organism localization, TAFII250, native protein, Stickstoff, natural protein, Saccharomyces diastaticus, Social Control, p230, Protein, Proteomes., DL-threo-1, TAF[[II]]250/230, TFIID, N-trimethylammonioacetate, establishment and maintenance of localization, Scc1, Library, CD148, DTL, Data Base, Saccharomyces oviformis, Taf[[II]]250, Yeast, DTT, TAF[[II]]230, UNQ26, Control, TAF[II]250, single-organism localization, azote, Understanding, Byp, Controls, CG17603, TAF[[II]], nitrogeno, Atlases, Protein Gene Products, Gene Proteins, R*)-1, Saccharomyces cerevisiae (Desm.) Meyen ex E.C. Hansen, DmelCG17603, nitrogen, localisation, Taf250, SR3-5, trimethylglycocoll, T160, regulation, N-trimethylammonio acetate, response, Baker's Yeast, 7N, PTPbeta2, RPTPJ, Regulation, 4-Dimercapto-2, Brewer's Yeast, Proteomes, N-trimethylmethanaminium inner salt, Baker Yeast, TAF230, establishment and maintenance of cellular component location, TAF1"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"S.cerevisiae - Whole organism, SC (Breker,j_cell_biol.,2013)","description":"abundance based on Spectral counting, Interaction consistency score: 11.0, Coverage: 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