{"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":["4565"],"full_dataset_link":["https://pax-db.org/dataset/4565/1786135094"],"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":["Presently, pearl millet and wheat are belonging to highly important cereal crops. Pearl millet, however, is an under-utilized crop, despite its superior resilience to drought and heat stress in contrast to wheat. To investigate this in more detail, we performed comparative physiological screening and large scale proteomics of drought stress responses in drought-tolerant and susceptible genotypes of pearl millet and wheat. These chosen genotypes are widely used in breeding and farming practices. The physiological responses demonstrated large differences in the regulation of root morphology and photosynthetic machinery, revealing a stay-green phenotype in pearl millet. Subsequent tissue-specific proteome analysis of leaves, roots and seeds led to the identification of 12,558 proteins in pearl millet and wheat under well-watered and stress conditions. To allow for this comparative proteome analysis and to provide a platform for future functional proteomics studies we performed a systematic phylogenetic analysis of all orthologues in pearl millet, wheat, foxtail millet, sorghum, barley, brachypodium, rice, maize, Arabidopsis, and soybean. In summary, we define (i) a stay-green proteome signature in the drought-tolerant pearl millet phenotype and (ii) differential senescence proteome signatures in contrasting wheat phenotypes not capable of coping with similar drought stress. These different responses have a significant effect on yield and grain filling processes reflected by the harvest index. Proteome signatures related to root morphology and seed yield demonstrated the unexpected intra- and interspecies-specific biochemical plasticity for stress adaptation for both pearl millet and wheat genotypes. These quantitative reference data provide tissue- and phenotype-specific marker proteins of stress defense mechanisms which are not predictable from the genome sequence itself and have potential value for marker-assisted breeding beyond genome assisted breeding."],"pubmed_title":["Physiological and Proteomic Signatures Reveal Mechanisms of Superior Drought Resilience in Pearl Millet Compared to Wheat."],"pubmed_authors":["Ghatak Arindam A, Chaturvedi Palak P, Bachmann Gert G, Valledor Luis L, Ramšak Živa Ž, Bazargani Mitra Mohammadi MM, Bajaj Prasad P, Jegadeesan Sridharan S, Li Weimin W, Sun Xiaoliang X, Gruden Kristina K, Varshney Rajeev K RK, Weckwerth Wolfram W"],"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"],"description_synonyms":["oho-31, l(2)144/1, bs29g06.y1, Dalpha2, OHO31, alphaKap2, CG4799, imp alpha2, Kap alpha2, Dimp-alpha2, pen, oho31, alpha2A-Kap, IMPalpha2, Kap-alpha2, imp-alpha2, importin alpha2/pendulin, DmelCG4799, pen-2, Imp-alpha2, DPend, Kpna2, l(2)k14401, 2.1, impalpha2, alpha2, anon-WO0140519.258., Rch1, Oho31"],"pubmed_title_synonyms":["Stress Immunity, Triticum durum, Grass, Immunity, Triticum vulgare, Fountaingrasses, Pearl Millets, Pearl Millet, Bajra, Triticum turgidum subsp. durum, Resilient Responses, Triticum aestivum subsp. aestivum, Drought, Pennisetum americanum, Psychological Resilient Response, Pennisetums, Pennisetum typhoides, Fountain Grass, Grasses, Canadian hard winter wheat, Resilience, Pearl, Millet, cattail millet, Wheat, Psychological, Psychological Resiliency, Psychological Resilient, Fountain, Resiliences, Pennisetum glaucum, Resilient Response, Fountain Grasses, Durum, Triticum aestivum8, Triticum spelta, Triticum sativum, Triticum aestivam, Psychological Resilient Responses, Resiliencies, Stress Immunities, wheat, Resiliency, Tricum aestivum, pearl millet, Fountaingrass, bread wheat, Durum Wheats, bulrush millet, Psychological Resilience, Stress, Setaria glauca, Response, Durum Wheat, Bajras, Triticum turgidum, Millets, Pennistum glaucum, common wheat., Pennisetum typhoideum, Triticum aestivum"],"name_synonyms":["Elaiosomes, Embryo, seed, Diaspore, Plant Zygotes, Diaspores, Embryos, pyrene (narrow)., Zygotes, Plant, Plant Embryo, Plant Zygote, Zygote, Seed, Elaiosome, GRO:0005339, Plant Embryos"],"pubmed_abstract_synonyms":["author summary, Stress Immunity, scale tissue, Zea mays var. japonica, determination, A., LUC7A, Mbp1, Sorghum bicolor subsp. bicolor, Pearl Millet, histology, GRO:0005339, GRO:0005338, Drought, Breedings., Social Controls, Cardaminopsis, Mechanisms, Arabidopsis thalianas, Sorghum bicolor milo, milo, A. thalianas, Rices, symptoms, Kaffir Corns, Zea mays subsp. tunicata, cattail millet, Setaria italicas, Elaiosome, Sorghum halepense, myd, anatomy and histology, Formal Social Controls, Wheat, Psychological, Psychological Resiliency, portion of tissue, Kaffir Corn, seed, Pennisetum glaucum, Fountain Grasses, Genomes, Soybean, plant peltate hair, Indian corn, Corns, Foxtail, Mouse-ear Cress, Soy Beans, Tissue, Mbp-1, Plant Embryo, proteins, Futurology, Resiliencies, wheat, Resiliency, Mouse-ear, Tricum aestivum, common wheat, Social, Chaetochloa italicas, climbing root (narrow), Diaspores, Psychological Resilience, Durum Wheat, Bajras, Triticum turgidum, Hordeum vulgare L., Zea, Arabidopses, Zea mays subsp. indurata, Asian cultivated rice, Predictions and Projections, broomcorn, screening, tolerant, sorghum, Soybeans, Zea mays subsp. amylacea, anatomical protrusion, gyltl1b-b, Triticum vulgare, Immunity, CROP, Crop, aerial root (narrow), Bajra, Triticum turgidum subsp. durum, A. thaliana, Resilient Responses, Kafir, Sudangrass, Pennisetum americanum, Sorghums, Soy Bean, Psychological Resilient Response, Bristlegrasses, Screenings, MDDGA6, Teosinte, mKIAA0609, Zea mays subsp. everta, Pearl, red rice, tissue portion, Millet, simple tissue, Sorghum halepenses, Sorghum saccharatum, Seed, Sorghum nervosum, KIAA0609, Setaria italica (L.) P.Beauv., Setaria Plants, Panicum italicum, Zea mays mays, fg, Italian, Psychological Resilient, Diaspore, Zea mays subsp. sacharata, German Millet, gyltl1b, Foxtail Millet, craw, Pennisetum macrochaetum, Phaseolus max, Setaria viridis subsp. italica, CREAP-1, Andropogon sorghum, Triticum sativum, mdc1d, expanded, Control, Plant, Sorghum bicolor, signs, Psychological Resilient Responses, Plant Zygote, foxtail millet, root, whole genome, Controls, Johnsongrass, Rice, summary, Phenotypes, cv. Wye, MDC1D, pearl millet, Fountaingrass, Arabidopsis, bulrush millet, enr, Agricultural, enlarged, Breedings, spine, rice, Setaria glauca, Zea ramosa, Indian, Regulation, Proteomes, Triticum aestivum, Sudangrasses, hLuc7A, big, Regulations, Agronomies, Johnsongrasses, Peptidomics, peltate hair, Zea mays subsp. ceratina, number, Pearl Millets, Gene, Agronomy, Development, Triticum aestivum subsp. aestivum, Setaria italica, presence, froggy, Gyltl1a, halepenses, protrusion, Hemisorghum, two-rowed barley, large, morphology, Chaetochloa italica, Sorghum, Fountain Grass, Grasses, Plants, susceptible, Mass, Gene Products, thalianas, Screening, Projections and Predictions, Foxtail Millets, Kafirs, RGD1307981, Farming, Chaetochloa, anatomy, Resilient Response, German, Maize, Cresses, MDDGB6, Triticum aestivum8, Triticum spelta, soybeans, Triticum aestivam, Zygote, LARGE, Stress Immunities, soybean, Barley, BPFD#36, Hordeum vulgare, bread wheat, Bristlegrass, synopsis, great, maize, Zea mays subsp. ramosa, Defense, Zygotes, Beans, Cress, Italian Millet, Mouse ear, Millets, Pennistum glaucum, Soy, Elaiosomes, Triticum durum, data, Sorghum bicolors, false bromes, corn, findings, Grass, Formal Social Control, Fountaingrasses, OA48-18, Proteins, Arabidopsis thaliana, total expressed protein, bicolors, grain, all, Indian Corn, count in organism, Pennisetums, native protein, Zea mays var. sacharata, Pennisetum typhoides, Social Control, Mass Screenings, Embryos, Canadian hard winter wheat, chemical analysis, Protein, Resilience, sequence, CRA, Brachypodium distachyon, scales, domesticated barley, Embryo, Setaria, Fountain, Resiliences, scale, Durum, Bean, Oryza sativa, thaliana, Plant Embryos, Mouse-ear Cresses, italica, Kaffir, primary structure of sequence macromolecule, Protein Gene Products, Gene Proteins, Sorghum vulgare, Durum Wheats, red rice <Oryza sativa>, Corn, Plant Zygotes, barley, Indexes, Glycine max, Stress, Response, Zea mays var. mays, regulation, assay, Future, Horedum vulgare, Pennisetum typhoideum, Agricultural Development, pyrene (narrow)"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"Taestivum - Seed, NSAF (Ghataketal,frontplantsci2020)","description":"abundance based on NSAF, Interaction consistency score: 2.1, Coverage: 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