PAXDB

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http://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimary200OK0000ProteomicsChristian von Mering39947https://pax-db.org/dataset/39947/1579464798mering@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.Cultivated rice (Oryza sativa L.) is frequently exposed to multiple stresses, including Schizotetranychus oryzae mite infestation. Rice domestication has narrowed the genetic diversity of the species, leading to a wide susceptibility. This work aimed to analyze the response of two African rice species (Oryza barthii and Oryza glaberrima), weedy rice (O. sativa f. spontanea), and O. sativa cv. Nipponbare to S. oryzae infestation. Surprisingly, leaf damage, histochemistry, and chlorophyll concentration/fluorescence indicated that the African species present a higher level of leaf damage, increased accumulation of H2O2, and lower photosynthetic capacity when compared to O. sativa plants under infested conditions. Infestation decreased tiller number, except in Nipponbare, and caused the death of O. barthii and O. glaberrima plants during the reproductive stage. While infestation did not affect the weight of 1,000 grains in both O. sativa, the number of panicles per plant was affected only in O. sativa f. spontanea, and the percentage of full seeds per panicle and seed length were increased only in Nipponbare. Using proteomic analysis, we identified 195 differentially abundant proteins when comparing susceptible (O. barthii) and tolerant (Nipponbare) plants under control and infested conditions. O. barthii presents a less abundant antioxidant arsenal and is unable to modulate proteins involved in general metabolism and energy production under infested condition. Nipponbare presents high abundance of detoxification-related proteins, general metabolic processes, and energy production, suggesting that the primary metabolism is maintained more active compared to O. barthii under infested condition. Also, under infested conditions, Nipponbare presents higher levels of proline and a greater abundance of defense-related proteins, such as osmotin, ricin B-like lectin, and protease inhibitors (PIs). These differentially abundant proteins can be used as biotechnological tools in breeding programs aiming at increased tolerance to mite infestation.Oryza sativa cv. Nipponbare and Oryza barthii as Unexpected Tolerance and Susceptibility Sources Against Schizotetranychus oryzae (Acari: Tetranychidae) Mite Infestation.Buffon Giseli G, Blasi Édina Aparecida Dos Reis ÉADR, Lamb Thainá Inês TI, Adamski Janete Mariza JM, Schwambach Joséli J, Ricachenevsky Felipe Klein FK, Bertolazi Amanda A, Silveira Vanildo V, Lopes Mara Cristina Barbosa MCB, Sperotto Raul Antonio RAAdd, 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, ratioInfestations, Oryza breviligulata, susceptibility, Mites, Mite, Oryza sativa Nipponbare, Oryza sativa, Oryza sativa cultivar Nipponbare, Acariasis, Rice, African wild rice, mites & ticks, Spider Mites, red rice <Oryza sativa>, rice, Mite Infestation., Rices, red rice, Mange, Acarina, Spider, Nipponbare, Spider Mite, Asian cultivated rice, Infestationexact)., exact), hoja (Spanish, 葉 (Japanesebiochemical pathways, Oryza breviligulata, Anti Oxidants, deceased, Metabolic Process, Endopeptidase Inhibitor, Activity, Pflanze, Metabolic Concepts, Peptide Hydrolase Inhibitor, Cardiac Death, GRO:0005339, Prolin, End-Of-Life, prevention, MAGE-E1 antigen, viridiplantae, SUB, exact), diseases, DmelCG12298, Castor Bean Lectin, Protease Inhibitor, responsivity, Rices, L-Proline, Concepts, SCRAMBLED, diseases and disorders, Inhibitors, Metabolism Concept, Elaiosome, Hydrolase Inhibitors, Phenomenon, present in fewer numbers in organism, prevention and control, KIF20A, Phyllobilins, Infestations, increased, Anti Oxidant, seed, human disease, RCA60, reference sample, catabolism, Moods, panicle, P, Plant Embryo, End Of Life, plants, proteins, metabolic process resulting in cell growth, GRO:0005317, saporins, (2S)-pyrrolidine-2-carboxylic acid, PROLINE, genetic, preventive measures, Ricins, Ricin D, decreased, Peptidohydrolase Inhibitor, parasitemia, nigrin b, HCA1, Ricin I, Diaspores, Antioxidant, Mite Infestation, Anti-Oxidant Effect, biotransformation, Homo sapiens disease, stage, Catabolism, Asian cultivated rice, tolerant, Taming, preventive therapy, anatomical protrusion, wide/broad, Process, Peptidase Inhibitor, DL-Proline, land plants, metabolism resulting in cell growth, Antioxidants, familial, STRUBBELIG, Endogenous, B Chain, Peptide Peptidohydrolase, Oryza sativa cultivar Nipponbare, Anti-Oxidants, Programs, weight, Mite Infestation., DAMAGE, Hepatocellular carcinoma-associated protein 1, Hydrolase Inhibitor, red rice, Near-Death Experience, secretion, gelonin, Seed, Nipponbare, Diaspore, antioxidants, Antagonists, Determination of Death, prolinum, Plant, Plant Zygote, (-)-proline, exposed, (S)-pyrrolidine-2-carboxylic acid, 葉 (Japanese, adventitious shoot, Ricin Toxin, Rice, disease, wide, Endogenous Antioxidants, higher plants, Peptidase Inhibitors, Breedings, spine, rice, Antiproteases, A Chain, inherited genetic, Endopeptidase, Peptide Peptidohydrolase Inhibitor, mMage-e1, Inhibitor, L-pyrrolidine-2-carboxylic acid, accessory, Ricin B Chain, AT1G11140, Lectin, other disease, Mite, (-)-(S)-proline, Processes, Endopeptidase Inhibitors, Endogenous Antioxidant, L-alpha-pyrrolidinecarboxylic acid, developmental stage, antoxidant, Ricin A Chain, number, RCA 60, Gene, antioxydant, ectoparasitic disease, Protease, broad, Metabolic Processes, presence, supernumerary, Castor Bean, CG12298, African wild rice, protrusion, Cardiac, reduced, subnumerary, Metabolism, Anti-Oxidant, Chlorophylls, susceptible, pyrrolidine-2-carboxylic acid, Gene Products, disease or disorder, Mood, Protease Antagonist, rRNA N-glycohydrolase activity, Animal, Peptide Hydrolase, Anti-Oxidant Effects, Metabolism Phenomena, Ricinus Lectin, Infestation, primary metabolism, plantae, reactivity, ricin, Hpro, ribosomal ribonucleate N-glycosidase activity, mei-1794, 2-Pyrrolidinecarboxylic acid, Metabolic Concept, Zygote, AI847422, decreased number, Antagonist, non-neoplastic, (S)-2-pyrrolidinecarboxylic acid, RNA N-glycosidase activity, extruding from, Protease Antagonists, Antioxidant Activity, L Proline, momorcochin-S, Zygotes, disorder, Peptide Peptidohydrolase Inhibitors, SRF9, species, (S)-2-carboxypyrrolidine, rRNA N-glycosidase activity, African unspecified, constitutitional genetic, Pis, PIS, Controlled, Elaiosomes, Controlling, degradation, prolina, exits through, Affects, Oryza sativa Nipponbare, Alpha-dystrobrevin-associated MAGE Protein, Proteins, disorders, mirabilis antiviral protein, medical condition, Acariasis, Anti Oxidant Effect, Peptide, Concept, Metabolic Phenomena, STRUBBELIG-RECEPTOR FAMILY 9, Chlorophyll 740, Metabolism Concepts, Ricinus Toxin, count in organism, Ricin, Animal Taming, native protein, Embryos, Antioxidant Effect, Protein, post-mortem, proteomic analysis, Phenomena, proline, condition, Death, metabolism, Metabolic Phenomenon, Embryo, Anti Oxidant Effects, susceptibility, death, multicellular organism metabolic process, (-)-2-pyrrolidinecarboxylic acid, biodegradation, Metabolic, L-Prolin, RGD1560259, increased number, prophylaxis, Dub, Oryza sativa, Pis1, PIS1, Peptidohydrolase Inhibitors, Plant Embryos, hoja (Spanish, Protein Gene Products, present in greater numbers in organism, Gene Proteins, Antioxidant Effects, Peptidase, red rice <Oryza sativa>, single-organism metabolic process, Antiprotease, concentration, Plant Zygotes, control, cardinality, Toxin, Mange, Peptide Hydrolase Inhibitors, response, L-(-)-proline, hereditary, T19D16.8, SCM, pyrene (narrow), Anabolism, Ricinus0falseO.satival - Leaf, iBAQ; ISOQuant output (Buffonetal,frontplantsci.2021)abundance based on iBAQ; ISOQuant_output, Interaction consistency score: 7.1, Coverage: 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