{"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":["3827"],"full_dataset_link":["https://pax-db.org/dataset/3827/1343465408"],"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":["Plant-derived smoke plays a key role in seed germination and plant growth. To investigate the effect of plant-derived smoke on chickpea, a gel-free/label-free proteomic technique was used. Germination percentage, root/shoot length, and fresh biomass were increased in chickpea treated with 2000 ppm plant-derived smoke within 6 days. On treatment with 2000 ppm plant-derived smoke for 6 days, the abundance of 90 proteins including glycolysis-related proteins significantly changed in chickpea root. Proteins related to signaling and transport were increased; however, protein metabolism, cell, and cell wall were decreased. The sucrose synthase for starch degradation was increased and total soluble sugar was induced. The proteins for nitrate pathway were increased and nitrate content was improved. On the other hand, although secondary metabolism related proteins were decreased, flavonoid contents were increased. Based on proteomic and immuno-blot analyses, proteins related to redox homeostasis were decreased and increased in root and shoot, respectively. Furthermore, fructose‑bisphosphate aldolase was increased; while, phosphotransferase and phosphoglycero mutase were decreased in glycolysis. In addition, phosphoglyceraldehyde‑3‑phosphate dehydrogenase and glutamine synthetase related genes were up-regulated. These results suggest that plant-derived smoke improves early stage of growth in chickpea with the balance of many cascades such as glycolysis, redox homeostasis, and secondary metabolism.<h4>Biological significance</h4>The current study examined the effects of plant-derived smoke on root of chickpea seedlings using a gel-free/label-free proteomic technique. Based on functional categorization of results from proteomics, proteins related to glycolysis, signaling, transport, protein metabolism, cell wall, and cell were predominantly changed in chickpea. The proteins related to carbohydrate and nitrate pathways were increased, while, those of secondary metabolism were decreased. Physiological analysis indicated that flavonoid, total soluble sugar, and nitrate content were increased in root of chickpea treated with plant-derived smoke for 6 days. Moreover, accumulated protein abundance of glyceraldehyde‑3‑phosphate dehydrogenase and fructose-bisphosphate aldolase was in agreement with immuno-blot results, which suggests that glycolysis process might be enhanced in root of chickpea in response to plant-derived smoke."],"pubmed_title":["Proteomic analysis of the promotive effect of plant-derived smoke on plant growth of chickpea."],"pubmed_authors":["Rehman Ali A, Rehman Shafiq Ur SU, Khatoon Amana A, Qasim Muhammad M, Itoh Takafumi T, Iwasaki Yukimoto Y, Wang Xin X, Sunohara Yukari Y, Matsumoto Hiroshi H, Komatsu Setsuko S"],"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":["Art, l(2)01092, dll, DLL, dl, l(2)387, DmelCG3629, Ba., BcDNA:LP01770, 2.7, CG3629, E(Arp), En(Arp)"],"pubmed_title_synonyms":["plantae, development, Cicers, Garbanzos., Garbanzo, Chickpea, growth pattern, Chickpeas, arietinum, Cicer, non-developmental growth, Pflanze, proteomic analysis, postnatal development, postnatal growth, Plant, Cicer arietinum, growth and development, growth, Cicer arietinums, viridiplantae"],"name_synonyms":["all, aerial root (narrow), root, GRO:0005338, climbing root (narrow)."],"pubmed_abstract_synonyms":["Oxidases, Fructosemonophosphate Aldolase, Dehydrogenases, protein metabolism, 2 Phenyl Chromenes, Materials, Product, Chickpeas, determination, Metabolisms, Pflanze, postnatal development, Embden-Meyerhof, Fructosediphosphate Aldolase, hydrates de carbone, growth and development, Sucrose synthase 2, protein, GRO:0005338, Embden Meyerhof Parnas Pathway, glucide, Fructose 1, viridiplantae, Fructosediphosphate, secondary metabolite metabolism, carbohydrates, dmTAF[[II]]230, solute:solute exchange, nitrate(1-), Techniques, protein polypeptide chains, Fructose Biphosphate Aldolase, shoot axis, Roles, Method, Biological, glucido, Concepts, DGS, 1, Embden-Meyerhof Pathway, Kinase, 6-Bisphosphate, Biological Product, protein aggregate, Fs(3)Hor, IKKg, KEY, Key, Cell Walls, treatment, Reductases, Oxidoreductase, F15E12_14, DmelCG2684, Malted Grain, Kohlenhydrate, multicellular organismal protein metabolic process, Grain, Glutamate Ammonia Ligase, Biologic Drugs, TFIID TAF250, AtSUS2 protein, cel, Natural, Flavonoid, HAND, 2 Phenyl Benzopyran, Glutamate Ammonia Ligase (ADP), Fructose 1-Phosphate, Pathways, bHLHa28, proteins, F15E12.14, inhibition of homeostatic process, NTef2, Biological Drugs, Fructose Bisphosphate Aldolase, foot, hand, Ligase, Fructose 1-Phosphate Aldolase, Biological Medicine, Methodological Studies, DmelCG1106, climbing root (narrow), signaling process, Role Concepts, Glutamate-Ammonia, disease management, Sprouted, Therapies, Medicine, sucrose synthase 3, homeostasis, sucrose synthase 2, stage, Medicines, ATP Phosphotransferases, NO3(-), Cicer arietinums, Biologic Drug, viridiplantae., ATP, single organism signaling, GRO:0005300, forefoot of quadruped, Therapy, dTAF[[II]]230, Germinations, Pathway, anatomical protrusion, Biologic Products, anaerobic glycolysis, TAF200, aerial root (narrow), NO3, saccharides, 2-Phenyl-Benzopyrans, GLUTAMINE SYNTHETASE, Procedure, TAFII-250, Embden-Meyerhof-Parnas, TAF250/230, Fs(3)Sz11, Embden-Meyerhof-Parnas Pathway, 2 Phenyl Benzopyrans, DmIKKgamma, TAFII250, Plant Sprouts, Role Concept, paw, Redox, soluble, positive regulation of homeostatic process, Playthings and Play, single-organism transport, dIKK, Biopharmaceuticals, Kenny, Role, Plaything, Genetic Materials, Biologic Product, secondary metabolism, Seed, Genetic Material, Kohlenhydrat, Garbanzos, saccharidum, Transphosphorylases, Seeds, Oxidase, growth pattern, Biological Medicines, non-developmental growth, Biological Drug, IKK-gamma, Plant, Toys, Biologics, Methodological, root, CG17603, carbohidratos, Methodological Study, TAF[[II]], Treatments, Embden-Meyerhof pathway, CG1106, early, Seedling, carbohidrato, 2 Phenyl Chromene, Grains, Arabidopsis, DmelCG16910, glycolysis, Taf250, Material, spine, label, SR3-5, Horka, Fructose, CG2684, fore paw, Fs(3)Horka, small molecule transport, Cistron, a carbohydrate, glucidos, forefoot, Embden-Meyerhof Pathways, Oxidation Reduction, TAF230, 2-Phenyl-Benzopyran, Glutamine, secondary metabolite metabolic process, Plant Sprout, biological signaling, d230, Plays, Garbanzo, Procedures, Biologic Pharmaceuticals, Peptidomics, Dehydrogenase, carbohydrate, developmental stage, saccharide, ATGSR2, Gene, dTAFII250, protein-containing complex, EfW1, sucrose synthetase, Glutamine Synthetase, dIKK-gamma, protrusion, UDP-glucose-D-fructose-2-glycosyltransferase, method, Suc synthase1, starch catabolism, 6-Bisphosphate Aldolase, polypeptide chain, dmTAF1, Taf230, Metabolism, DmIKK-gamma, method used in an experiment, modified Embden-Meyerhof pathway, Sprouted Seed, Studies, germination, Gene Products, CG18144, DmF2, Malted, dmIKKgamma, IKK[[gamma]], Technique, AtSUS3 protein, Phosphotransferase, Walls, Toy, TAF250, Biologicals, plantae, lod, Drugs, study, Taf200, glutamine synthase clone F11, dTAF[[II]]250, Genetic, Playthings, cell, gel, dHand, Natural Product, 6-biphosphate D-glyceraldehyde-3-phosphate-lyase, Taf1p, Transphosphorylase, Aldolase B, Aldolase A, Dhand, L-Glutamate:ammonia ligase (ADP-forming), Study, dTAF250, Bioflavonoids, Puppets, hand-C, IKK, Sucrose-UDP glucosyltransferase, negative regulation of homeostatic process, Play, dHAND, TAF, Puppet, starch breakdown, NITRATE ION, Biologic, protein metabolism and modification, Sucrose-uridine diphosphate glucosyltransferase, Pharmaceuticals, Autoregulation, protein metabolic process and modification, Products, TAF[[II]]250, Embden Meyerhof Pathway, Malted Grains, arietinum, Biologic Medicines, protein complex, Proteins, l(3)84Ab, Bioflavonoid, BG:DS00004.13, Sucrose-UDP glucosyltransferase 2, Cistrons, Sprout, Cell, Phosphotransferases, Sucrose-UDP glucosyltransferase 1, Concept, all, dTAF230, starch degradation, Secondary Metabolisms, development, 2-Phenyl-Chromene, IKKgamma, Aldolase C, native protein, natural protein, p230, fore-paw, Protein, Fructosemonophosphate, chemical analysis, Biopharmaceutical, TAF[[II]]250/230, Synthetase, TFIID, Nitrate, Fructose Biphosphate, Fructose-Bisphosphate, forefeet, regulation of homeostatic process, glucides, 2-Phenyl-Chromenes, D-Fructose-1, Reductase, Taf[[II]]250, Wall, Sprouts, TAF[[II]]230, Dmikkgamma, Kinases, Fructose 1 Phosphate Aldolase, DmelCG18144, postnatal growth, Cicer arietinum, TAF[II]250, CG16910, Lds, Carbohydrate, Embden-Meyerhof-Parnas pathway, Aldolase, signalling, Sugar, plan specification, Protein Gene Products, Hands, Drug, Gene Proteins, Secondary, Cicers, Suc synthase 1, DmelCG17603, Sucrose synthase isoform I, activation of homeostatic process, [NO3](-), signalling process, Chickpea, Therapeutic, 6 Bisphosphate Aldolase, Biomasses, Cicer, fore foot, Sprouted Seeds, forepaw, Natural Products, Treatment, assay, Class II, growth, Uridine diphosphoglucose-fructose glucosyltransferase, 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