{"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":["3847"],"full_dataset_link":["https://pax-db.org/dataset/3847/240311872"],"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":["Tungsten (W) finds increasing application in military, aviation and household appliance industry, opening new paths into the environment. Since W shares certain chemical properties with the essential plant micronutrient molybdenum (Mo), it is proposed to inhibit enzymatic activity of molybdoenzymes [e.g., nitrate reductase (NR)] by replacing the Mo-ion bound to the co-factor. Recent studies suggest that W, much like other heavy metals, also exerts toxicity on its own. To create a comprehensive picture of tungsten stress, this study investigated the effects of W on growth and metabolism of soybean (<i>Glycine max</i>), depending on plant nitrogen regime [nitrate fed (N fed) vs. symbiotic N<sub>2</sub> fixation (N fix)] by combining plant physiological data (biomass production, starch and nutrient content, N<sub>2</sub> fixation, nitrate reductase activity) with root and nodule proteome data. Irrespective of N regime, NR activity and total N decreased with increasing W concentrations. Nodulation and therefore also N<sub>2</sub> fixation strongly declined at high W concentrations, particularly in N fix plants. However, N<sub>2</sub> fixation rate (g N fixed g<sup>-1</sup> nodule dwt) remained unaffected by increasing W concentrations. Proteomic analysis revealed a strong decline in leghemoglobin and nitrogenase precursor levels (NifD), as well as an increase in abundance of proteins involved in secondary metabolism in N fix nodules. Taken together this indicates that, in contrast to the reported direct inhibition of NR, N<sub>2</sub> fixation appears to be indirectly inhibited by a decrease in nitrogenase synthesis due to W induced changes in nodule oxygen levels of N fix plants. Besides N metabolism, plants exhibited a strong reduction of shoot (both N regimes) and root (N fed only) biomass, an imbalance in nutrient levels and a failure of carbon metabolic pathways accompanied by an accumulation of starch at high tungsten concentrations, independent of N-regime. Proteomic data (available via ProteomeXchange with identifier PXD010877) demonstrated that the response to high W concentrations was independent of nodule functionality and dominated by several peroxidases and other general stress related proteins. Based on an evaluation of several W responsive proteotypic peptides, we identified a set of protein markers of W stress and possible targets for improved stress tolerance."],"pubmed_title":["Molecular Mechanisms of Tungsten Toxicity Differ for <i>Glycine max</i> Depending on Nitrogen Regime."],"pubmed_authors":["Preiner Julian J, Wienkoop Stefanie S, Weckwerth Wolfram W, Oburger Eva E"],"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":["soybean, Soy Bean, cv. Wye, Soybeans, Wolfram, nitrogen, Stickstoff, nitrogeno., Phaseolus max, Soybean, Glycine max, N, Bean, soybeans, margin of safety, Soy Beans, Beans, toxic potential, 7N, azote, Soy"],"name_synonyms":["shoot axis, GRO:0005300."],"pubmed_abstract_synonyms":["Force Personnel, Metabolic Networks, Ideal, chemical properties, ion, FON1, Metabolisms, Tertiary Sectors, Metabolic Concepts, growth and development, One-Person Households, FLORAL ORGAN NUMBER 1, Average Family Sizes, secondary metabolite metabolism, 5730420M11Rik, Polypeptides, protein polypeptide chains, shoot axis, Abnormal retropulsion test, DmelCG12298, Carbon-12, oxigeno, Ideal Family Size, SCRAMBLED, Metabolism Concept, Nutrient, nodule morphogenesis, C, SET, ostium, Theory, Utility Theories, Soybean, nitrite:acceptor oxidoreductase, Personnel, catabolism, anabolism, N, O, Oxygen-16, Bdr, Economic Policies, Armed Forces, Pathways, metabolic process resulting in cell growth, proteins, Living Costs, SNAP-25, DmelCG4299, Oxygen, set, Average, [OO], climbing root (narrow), Household Consumptions, Economic, Heavy, Soldiers, Pathway, chemical characterization, Indices, Index, metabolism resulting in cell growth, land plants, STRUBBELIG, aerial root (narrow), alpha-lecithin cholesterol acyltransferase deficiency, Household and Family, Parachuting, T32E8.9, Vitreous, Economic Condition, Stickstoff, Utility Theory, margin of safety, Completed Family Size, nitrate reductase (acceptor), GENA70, secretion, Macroeconomic, secondary metabolism, respiratory nitrate reductase activity, Amylomaize, Couples, dioxygen, HLA-DR-associated protein II, DI-2, I-2Dm, Family Demographies, Consumer Price Indices, root, NITRATE REDUCTASE, Home, Condition, I-2PP1, higher plants, Sector, nitrogen, TAF-IBETA, AKL3L, Household Head, root tubercle, TAF-Ibeta, Nitrogenase, Dioxygen, FLORAL DEFECTIVE 10, Traffic Control, secondary metabolite metabolic process, Policies, Sectors, LCATA deficiency, nodule, Processes, Utility, E-948, SUPERMAN, biosynthesis, precursor, Metabolic Processes, protein-containing complex, Easterlin, One Person Household, Submariners, Air, Gene Products, nitrate reductase 1, Partial LCAT deficiency, dyslipoproteinemic corneal dystrophy, Industries, plantae, Dinitrogenase, AK6, mei-1794, soybeans, nutrients, Reduced ferredoxin:dinitrogen oxidoreductase (ATP-hydrolysing), Metabolic Concept, 2pp2a, Microeconomic Factors, ions, CG10574, soybean, synthesis, Households, GNR1, 2PP2A, Capital, dSET, dSet, Beans, peptidos, chemical structure, Soy, chemical composition, NITRATE ION, Macronutrient, foramen, Oxygen 16, degradation, Conditions, Proteins, Family Demography, Factor, nitrite:(acceptor) oxidoreductase, Synaptosomal-associated 25 kDa protein, nitrite - acceptor oxidoreductase, micronutrients, carbone, oxygen, Submariner, Concept, all, Macronutrients, Secondary Metabolisms, carbono, Army, Quinol-Nitrate Oxidoreductase, Wolfram, Tertiary, Leghemoglobin A, native protein, Consumer Price Index, Consumer Price, I-2PP2A, Dm I-2, proteomic analysis, Nitrate, oxygene, metabolism, OXYGEN MOLECULE, Metabolic Pathways, Air Force, Metabolic Phenomenon, Reductase, O2, multicellular organism metabolic process, ensemble, Ovoperoxidase, alpha-LCAT deficiency, Dub, postnatal growth, Family Life Surveys, azote, nitrite - (acceptor) oxidoreductase, Gene Proteins, Biomasses, opening, Glycine max, Air Traffic Control, Completed, E 948, General activity, Anabolism, biochemical pathways, Networks, IPP2A2, Metabolic Process, Activity, Pflanze, postnatal development, Amylum, protein, GRO:0005338, viridiplantae, SUB, nitrate(1-), peptido, Household Heads, SUP, Head of Household, Concepts, Impacts, Environmental Impacts, E948, protein aggregate, Phenomenon, Microeconomic, KIF20A, Family and Household, multicellular organismal biosynthetic process, single-organism biosynthetic process, Oxidoreductase, peptides, Household Consumption, TAF-I, Expected Family Sizes, Soy Beans, plants, Super protein, Family Life Survey, sp, Military, Environmental Impact, IGAAD, Family Life, Starch, Completed Family Sizes, DmelCG10574, Respiratory, Carbon, Respiratory Nitrate Reductase, fish-eye disease, biotransformation, One-Person, Theories, NO3(-), ostia, Catabolism, Desired, Generations, GRO:0005300, phapii, Soybeans, Home Economics, Vanadium, Process, Metal, Air Traffic, Coast Guard, Hypothesis, NO3, StF-IT-1, Navy Personnel, Metabolic Network, foramina, Sailor, Macroeconomic Factors, Economics, Expected, Soy Bean, lymhpoid nodule, Household, Quinol Nitrate Oxidoreductase, Ionen, Sauerstoff, T32E8_9, Ideal Family Sizes, Army Personnel, parent ion, Disauerstoff, Factors, growth pattern, Phaseolus max, Respiratory Nitrate, non-developmental growth, 6C, Control, Plant, CG4299, chemical content, cv. Wye, Nitrate Reductase, Vitreous Carbon, Easterlin Hypothesis, precursor ion, NR1, carbonium, Micronutrient, Heavy Metal, Heavy Metals, Polypeptide, 7N, i2pp2a, Proteomes, Remittances, AT1G11140, Desired Family Sizes, Molybdenum-98, Amylomaize Starch, Air Force Personnel, Gene, Family Sizes, carbon, 8O, Network, AKL3L1, Sailors, Cornstarch, PHAPII, CG12298, alpha-lecithin:cholesterol acyltransferase deficiency, Vanadium Nitrogenase, dioxygene, polypeptide chain, Metabolism, Survey, Imbalance, Metabolism Phenomena, study, NITRATE REDUCTASE 1, formation, iones, ipp2a2, Soldier, Economic Conditions, Family Size, Mif1, FED, Kohlenstoff, taf-ibeta, toxic potential, SRF9, Family, Desired Family Size, Family Characteristic, molecular oxygen, Policy, Economic Policy, Gene., nutrient, data, protein complex, synthesize, igaad, One-Person Household, total expressed protein, Production, Expected Family Size, Living Cost, Peptide, group, Armed Forces Personnel, Impact, Metabolic Phenomena, Consumption, STRUBBELIG-RECEPTOR FAMILY 9, Environmental, development, Metabolism Concepts, natural protein, Keoflo, Protein, Phenomena, I2PP2A, Average Family Size, Demography, biodegradation, Metabolic, Bean, trace elements, FLO10, AK3L1, HERP, Molybdenum 98, nitrogeno, Carbon 12, Protein Gene Products, Secondary, dSET/TAF-Ibeta, single-organism metabolic process, 2610030F17Rik, [NO3](-), Remittance, Ion, Marines, SNAP, Cost of Living, Environments, Navy, Metabolic Pathway, Tertiary Sector, Peptid, FIX, Quinol-Nitrate, AA407739, growth, T19D16.8, SCM"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"Gmax - Shoot, iBAQ (Preineretal,frontplantsci2019)","description":"abundance based on iBAQ, Interaction consistency score: 8.6, Coverage: 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