PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimary200OK0000ProteomicsChristian von Mering449447https://pax-db.org/dataset/449447/3141380789mering@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.Toxin production in algal blooms presents a significant problem for the water industry. Of particular concern is microcystin, a potent hepatotoxin produced by the unicellular freshwater species Microcystis aeruginosa. In this study, the proteomes of six toxic and nontoxic strains of M. aeruginosa were analyzed to gain further knowledge in elucidating the role of microcystin production in this microorganism. This represents the first comparative proteomic study in a cyanobacterial species. A large diversity in the protein expression profiles of each strain was observed, with a significant proportion of the identified proteins appearing to be strain-specific. In total, 475 proteins were identified reproducibly and of these, 82 comprised the core proteome of M. aeruginosa. The expression of several hypothetical and unknown proteins, including four possible operons was confirmed. Surprisingly, no proteins were found to be produced only by toxic or nontoxic strains. Quantitative proteome analysis using the label-free normalized spectrum abundance factor approach revealed nine proteins that were differentially expressed between toxic and nontoxic strains. These proteins participate in carbon-nitrogen metabolism and redox balance maintenance and point to an involvement of the global nitrogen regulator NtcA in toxicity. In addition, the switching of a previously inactive toxin-producing strain to microcystin synthesis is reported.Comparative protein expression in different strains of the bloom-forming cyanobacterium Microcystis aeruginosa.Alexova Ralitza R, Haynes Paul A PA, Ferrari Belinda C BC, Neilan Brett A BAAdd, 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, ratioSu(tor)2-2, BG:DS00941.4, CG7793, 34Ea, l(2)k05224, E(var)189, l(2)k06321, EY2-3, dme-SOS, l(2)Sos, l(2)34Ea, sos, SOS, 2.3, EK2-8, DmelCG7793, E(sev)2A, br24, l(2)br25, l(2)br24., dSos, br25, Sos1Protein Gene Products, Gene Proteins, Microcystis aeruginosa, protein polypeptide chains, native protein, natural protein, polypeptide chain, protein complex, Protein, Strain, Gene Products, Proteins, Sprain, Micraloa aeruginosa., Gene, Strains, proteins, protein, protein aggregate, protein-containing complex, Sprains, Strains and Sprainsl(3)Ca, multi-cellular organism, body, mCRY, titin, whole body, 26S protease, l(3)62Ca, d-titin, 0020/01, threonine endopeptidase activity, Mbh1, SLS, Sls, ingensin, kettin, organism, large multicatalytic protease, CFU-MC, HEL-S-66, DmelCG1915, Titin, prosome, Crry, multicatalytic endopeptidase complex, animal, anon-CREST, Ket, CFU-Mast, tricorn proteinase, D-titin, l(3)j1D7, whole organism, AFCP, colony forming unit mast cell, D-Titin, CG18857, MIC10, ket, sam, sal, TLX, l(3)dre8, lens neutral proteinase, CG1915, CT41299, multicatalytic proteinase (complex), Koerper, proteasome endopeptidase complex., KZ, polyhedral organelle, l(3)S002001, l(3)rL182, CG18242, tricorn protease, AHUS2, TRA2.10, Mcp, MCP, alkaline protease, multicatalytic proteinase, CG18245Water, biochemical pathways, Metabolic Process, determination, PNT-P1, DmelCG17077, Tertiary Sectors, Metabolic Concepts, Mbp1, Algal Blooms, BOUND WATER, EY3-1, protein, Pnt, HOH, protein polypeptide chains, Micraloa aeruginosa, png, Roles, Carbon-12, Concepts, Blooms, Bloom, Metabolism Concept, D-ets-2, 3520, protein aggregate, myd, Phenomenon, Microeconomic, Pnt-P1, Freshwaters, C, single-organism biosynthetic process, Theory, Utility Theories, Household Consumption, catabolism, anabolism, N, Economic Policies, Mbp-1, proteins, metabolic process resulting in cell growth, Living Costs, ecotype, Waters, Carbon, Role Concepts, dihydridooxygen, Household Consumptions, biotransformation, Economic, Strains, Theories, dihydrogen oxide, Catabolism, NTCA, Home Economics, Indices, Index, Process, gyltl1b-b, Hypothesis, metabolism resulting in cell growth, aqua, D-Ets-2, ets94F, 0123/09, Macroeconomic Factors, Economics, Vitreous, H2O, Economic Condition, Household, Role Concept, Redox, Operons, Stickstoff, Utility Theory, MDDGA6, mKIAA0609, Role, margin of safety, secretion, Macroeconomic, cultivar, KIAA0609, regulator, Hydrogen Oxide, fg, Epistemology, pntP2, Factors, gyltl1b, Pointed-P1, Freshwater, 6C, Consumer Price Indices, mdc1d, Ets94F, hydrogen hydroxide, expanded, Home, acqua, Condition, ptd, Microcystis aeruginosa, MDC1D, PntP2, Vitreous Carbon, Sector, nitrogen, Easterlin Hypothesis, enr, enlarged, label, PntP1, E(E2F)3D, carbonium, PNTP2, Wasser, 7N, Strains and Sprains, Proteomes, PNTP1, Oxidation Reduction, Remittances, Fresh, big, Policies, 0998/12, Sectors, multicellular organismal biosynthetic process., Processes, ETS2, Ets2, nucleocapsid, Utility, Gene, carbon, biosynthesis, Metabolic Processes, protein-containing complex, froggy, agua, Gyltl1a, Easterlin, large, DMPOINT1A, pntegfr, 0608/07, polypeptide chain, Metabolism, Gene Products, toxins, Sprains, Metabolism Phenomena, Industries, study, pointed-RC, formation, MDDGB6, Algal Bloom, Metabolic Concept, Microeconomic Factors, LARGE, eau, Economic Conditions, Maintenances, EK3-2, synthesis, Algal, BPFD#36, l(3)07825, Kohlenstoff, Capital, great, CG17077, toxic potential, species, l(3)j1B7, Policy, Economic Policy, Ets, degradation, protein complex, synthesize, Conditions, Sprain, Proteins, 3-nitroso-, total expressed protein, Factor, Production, Living Cost, carbone, Consumption, Concept, strain, Metabolic Phenomena, carbono, Metabolism Concepts, Tertiary, native protein, Consumer Price Index, natural protein, Consumer Price, Protein, chemical analysis, Strain, Phenomena, core, 4-Thiazolidinecarboxylic acid, metabolism, pnt-P1, pnt-P2, l(3)s118306, Metabolic Phenomenon, Eutrophications, multicellular organism metabolic process, Fresh Waters, biodegradation, Metabolic, azote, Carbon 12, nitrogeno, Protein Gene Products, Gene Proteins, single-organism metabolic process, Ets58AB, Remittance, Cost of Living, Tertiary Sector, assay, [OH2], POINT, Anabolism, CG87050falseM.aeruginosa - Whole organism, Uwoccmrd, SC (Alexova,mcp,2011)abundance based on Spectral counting UWOCCMRD, UWOCCMRD, Interaction consistency score: 2.3, Coverage: 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