PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering4932https://pax-db.org/dataset/4932/3388877431mering@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.A major goal of biology is to provide a quantitative description of cellular behaviour. This task, however, has been hampered by the difficulty in measuring protein abundances and their variation. Here we present a strategy that pairs high-throughput flow cytometry and a library of GFP-tagged yeast strains to monitor rapidly and precisely protein levels at single-cell resolution. Bulk protein abundance measurements of >2,500 proteins in rich and minimal media provide a detailed view of the cellular response to these conditions, and capture many changes not observed by DNA microarray analyses. Our single-cell data argue that noise in protein expression is dominated by the stochastic production/destruction of messenger RNAs. Beyond this global trend, there are dramatic protein-specific differences in noise that are strongly correlated with a protein's mode of transcription and its function. For example, proteins that respond to environmental changes are noisy whereas those involved in protein synthesis are quiet. Thus, these studies reveal a remarkable structure to biological noise and suggest that protein noise levels have been selected to reflect the costs and potential benefits of this variation.Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise.Newman John R S JR, Ghaemmaghami Sina S, Ihmels Jan J, Breslow David K DK, Noble Matthew M, DeRisi Joseph L JL, Weissman Jonathan S JSAdd, 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, ratioProtein Gene Products, Gene Products, Proteins, Gene Proteins, data, Gene, proteins, native protein, Protein., ProteindTAF[[II]]230, TAF[[II]]250, d230, Noise, Saccharomyces cerevisiae 'var. diastaticus', TAF200, Brewer's, Pollution, l(3)84Ab, baker's yeast, dTAFII250, BG:DS00004.13, Noises., TAFII-250, TAF250/230, EfW1, Cell, Saccharomyces italicus, Saccaromyces cerevisiae, dTAF230, dmTAF[[II]]230, Baker's Yeasts, Sccharomyces cerevisiae, TAFII250, dmTAF1, Saccharomyces diastaticus, Taf230, p230, yeast, proteomic analysis, TAF[[II]]250/230, TFIID, lager beer yeast, TAF250, Saccharomyces oviformis, Taf[[II]]250, Yeast, Taf200, dTAF[[II]]250, TAF[[II]]230, TFIID TAF250, cel, cell, Saccharomyes cerevisiae, Taf1p, TAF[II]250, Baker, CG17603, Saccharomyces uvarum var. melibiosus, TAF[[II]], S. cerevisiae, dTAF250, Saccharomyces cerevisiae (Desm.) Meyen ex E.C. Hansen, S cerevisiae, DmelCG17603, Candida robusta, Taf250, Saccharomyces capensis, SR3-5, Baker's, Mycoderma cerevisiae, 1883, Noise Pollution, Baker's Yeast, brewer's yeast, TAF, Brewer's Yeast, TAF230, Baker Yeast, TAF1Protein Gene Products, Gene Proteins, organism, multi-cellular organism, whole organism, native protein, data., body, Koerper, Protein, Gene Products, Proteins, Gene, whole body, proteins, animalprotein translation, protein levels, d230, conformation, number, Goal, Gene, baker's yeast, DNA Microchips, dTAFII250, DNA Arrays, protein, Noises., protein-containing complex, EfW1, presence, Saccharomyces italicus, Fluorescence-Activated, dmTAF[[II]]230, protein polypeptide chains, Fluorescence-Activated Cell Sortings, Microfluorometry, polypeptide chain, dmTAF1, Taf230, yeast, CG9063, Gene Products, Flow Microfluorimetry, DNA Chip, protein aggregate, Cell Sortings, Sprains, cDNA Microarray, Arrays, Microchip, lager beer yeast, Cytofluorometry, TAF250, Taf200, dTAF[[II]]250, TFIID TAF250, Oligonucleotide Microarrays, Fluorescence Activated Cell Sorting, Flow Cytofluorometries, cel, cDNA Microarrays, cell, Chip, Microfluorometries, Microchips, Saccharomyes cerevisiae, Taf1p, proteins, Dietary Fiber, Saccharomyces uvarum var. melibiosus, BcDNA:GH03694, cDNA Arrays, K2p3.1, dTAF250, Chips, Candida robusta, Saccharomyces capensis, scientific observation, Flow, Flow Microfluorometries, Oligonucleotide Microarray, Cytometry, Oligonucleotide Arrays, DNA Array, Strains, brewer's yeast, TAF, transcription from bacterial-type RNA polymerase promoter, relational structural quality, Flow Cytofluorometry, DmelCG9063, Cytometries, Sortings, single-organism behavior, measuring, Cell Sorting, data, protein anabolism, dTAF[[II]]230, TAF[[II]]250, Noise, Fluorescence-Activated Cell Sorting, protein biosynthetic process, OAT1, protein complex, Microarray, Gene Chip, Proteins, Sprain, TAF200, Pollution, l(3)84Ab, Flow Cytometries, BG:DS00004.13, DNA-array, function, TAFII-250, TAF250/230, cDNA, Oligonucleotide, Saccaromyces cerevisiae, Cell, dTAF230, Microfluorimetry, TASK, Sccharomyces cerevisiae, Oligonucleotide Array, count in organism, DNA Chips, TAFII250, Microarrays, TBAK1, native protein, natural protein, p230, Gene Chips, Protein, Strain, protein formation, TAF[[II]]250/230, TFIID, protein biosynthesis, Flow Microfluorometry, Library, DNA Microarray, Saccharomyces oviformis, Taf[[II]]250, Yeast, cDNA Array, Cytofluorometries, TAF[[II]]230, PPH4, BcDNAGH03694, TAF[II]250, CG17603, Fluorescence-Activated Cell, TAF[[II]], 3L6, Noises, Protein Gene Products, Gene Proteins, DNA Microarrays, DmelCG17603, Gene Expression Microarray Analysis, Taf250, rich, protein synthesis, SR3-5, bacterial transcription, Sorting, Array, Noise Pollution, DNA, TASK-1, Oligodeoxyribonucleotide Array Sequence Analysis, Strains and Sprains, Sequence Analysis, TAF230, DNA Microchip, TAF10falseS.cerevisiae - Whole organism, Intensity of gfp-tagged proteins, SD normalized data (Newman,nature,2006)abundance based on SD normalized data, intensity of GFP-tagged proteins, Interaction consistency score: 7.5, Coverage: 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