PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering4932https://pax-db.org/dataset/4932/527300760mering@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.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).A novel single-cell screening platform reveals proteome plasticity during yeast stress responses.Breker Michal M, Gymrek Melissa M, Schuldiner Maya MAdd, 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, ratioscreening, 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, TAF1Taf[[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, TAF250Bret, 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, TAF10falseS.cerevisiae - Whole organism, SC (Breker,j_cell_biol.,2013)abundance based on Spectral counting, Interaction consistency score: 11.0, Coverage: 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