{"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"},"statusCodeValue":200,"statusCode":"OK"}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Christian von Mering"],"species":["39947"],"full_dataset_link":["https://pax-db.org/dataset/39947/600882001"],"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":["<h4>Unlabelled</h4>Rice is the major staple food for more than half of world's population. As global climate changes, we are observing more floods, droughts and severe heat waves. Two rice cultivars with contrasting genetic backgrounds and levels of tolerance to drought, Nipponbare and IAC1131, were used in this study. Four-week-old seedlings of both cultivars were grown in large soil volumes and then exposed to moderate and extreme drought for 7days, followed by 3days of re-watering. Mature leaves were harvested from plants from each treatment for protein extraction and subsequent shotgun proteomic analysis, with validation of selected proteins by western blotting. Gene Ontology (GO) annotations of differentially expressed proteins provide insights into the metabolic pathways that are involved in drought stress resistance. Our data indicate that IAC1131 appears to be better able to cope with stressful conditions by upregulating a suite of stress and defence response related proteins. Nipponbare, in contrast, lacks the range of stress responses shown by the more stress tolerant variety, and responds to drought stress by initiating a partial shutdown of chlorophyll biosynthesis in an apparent attempt to preserve resources.<h4>Significance</h4>In this study, two rice genotypes with contrasting drought tolerance were exposed to soil water deficits, and proteomic changes were observed in mature leaf laminae. Plants were well watered and then switched to conditions of either moderate drought or extreme drought followed by three days of recovery. Proteins were identified and quantified using both label-free and Tandem Mass Tag multiplexing approaches. Several biochemical pathways were significantly altered in response to water deficit. Most notably, the up-regulation of ClpD1 protease responded strongly in the drought-tolerant landrace; this protein is typically involved in heat and osmotic stress response. In contrast, porphyrin and chlorophyll biosynthesis pathways were down-regulated, indicating suppression of the photosynthetic machinery."],"pubmed_title":["Quantitative proteomic analysis of two different rice varieties reveals that drought tolerance is correlated with reduced abundance of photosynthetic machinery and increased abundance of ClpD1 protease."],"pubmed_authors":["Wu Yunqi Y, Mirzaei Mehdi M, Pascovici Dana D, Chick Joel M JM, Atwell Brian J BJ, Haynes Paul A PA"],"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":["small, increased, Drought Resistances, Injury, underdeveloped, Drought Escapes, Recovery, number, Oryza sativa, hypoplasia, Drought Avoidences, increased number., presence, Drought, supernumerary, Rice, present in greater numbers in organism, Drought Tolerances, count in organism, red rice <Oryza sativa>, Drought Recovery, Drought Tolerance, Tolerance, reduced, rice, Rices, proteomic analysis, red rice, Resistance, Drought Injury, Drought Recoveries, Drought Injuries, tiny, drought tolerance, Drought Escape, Asian cultivated rice, Avoidence, Drought Avoidence, accessory"],"name_synonyms":["exact)., exact), hoja (Spanish, 葉 (Japanese"],"pubmed_abstract_synonyms":["biochemical pathways, Metabolic Networks, Networks, chlorophyll formation, Gene Ontology Projects, Drought Escapes, Mbp1, BOUND WATER, protein, Drought, CG11121, osmotic response, HOH, School-Age, protein polypeptide chains, old, exact), Catastrophic Flooding, Rices, Alleviating interaction, Project, protein aggregate, myd, WMS, treatment, Osmotic Stress, Malted Grain, Grain, catabolism, Mbp-1, Pathways, plants, proteins, SO, free, genetic, chlorophyll biosynthesis, Drought Recovery, Drought Tolerance, Sprouted, disease management, Therapies, dihydridooxygen, Drought Injury, biotransformation, Catastrophic, Porphyrin, dihydrogen oxide, drought tolerance, GPHYSD2, Asian cultivated rice, So, Avoidence, SGS, Therapy, close to, tolerant, Pathway, anatomical protrusion, gyltl1b-b, land plants, familial, aqua, Up-Regulation (Physiology), Metabolic Network, Oryza sativa cultivar Nipponbare, ACMICD, H2O, Plant Sprouts, School Age, MDDGA6, mKIAA0609, Responses, red rice, defence response, Ontology Projects, secretion, Seed, Nipponbare, KIAA0609, Osmotic Stress Responses, Hydrogen Oxide, suppressive genetic interaction (sensu inequality)., fg, Gene Ontologies, Populations, Seeds, Ontology, Stress Response, gyltl1b, Ontologies, Projects, Upregulation, mdc1d, Plant, expanded, hydrogen hydroxide, MASS, exposed, Treatments, 葉 (Japanese, acqua, Rice, Seedling, MDC1D, Drought Tolerances, Grains, higher plants, Health, enr, Tolerance, enlarged, spine, label, rice, chlorophyll synthesis, inherited genetic, School-Age Population, Wasser, Osmotic Stress Regulating Pathway, Drought Avoidence, osmotic stress response, big, Plant Sprout, Drought Resistances, Floodings, Health Resource, FBN, Gene, Network, chlorophyll anabolism, protein-containing complex, response to water stimulus, Gene Ontology Project, froggy, Gene Ontology, Gyltl1a, agua, protrusion, large, polypeptide chain, DmelCG11121, ECTOL1, Flooding, Peat, resistance, Sprouted Seed, Gene Products, Malted, Drought Injuries, Resources, School-Age Populations, study, somda, Injury, Receptor Up-Regulation, MDDGB6, Up Regulation, Humus, Drought Avoidences, Osmotic, LARGE, eau, Population, OCTD, BPFD#36, Climates, extruding from, Stress Responses, great, Soils, School Age Population, constitutitional genetic, TAG, Catastrophic Floodings, Drl, data, Malted Grains, degradation, defense/immunity protein activity, protein complex, Recovery, exits through, Oryza sativa Nipponbare, Proteins, Laminae, Sprout, antimicrobial peptide activity, Mdu, near to, epsilon-COP, native protein, Resource, natural protein, mda, Protein, proteomic analysis, Resistance, Drought Recoveries, MFS1, Osmotic Stress Response, Foods, ami, Metabolic Pathways, WMS2, Ontology Project, covalent modifier, Sprouts, physiological defense response, biodegradation, Metabolic, med, Oryza sativa, School Age Populations, hoja (Spanish, Protein Gene Products, Gene Proteins, red rice <Oryza sativa>, Therapeutic, approaches, SSKS, vicinity of, Sprouted Seeds, Response, Metabolic Pathway, Treatment, earth, [OH2], hereditary, Drought Escape, Severe"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"O.satival - Leaf, NSAF (Wuetal.,journalofproteomics2016)","description":"abundance based on NSAF, Interaction consistency score: 7.5, Coverage: 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