{"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/3847/1643956961"],"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":["Salinity severely threatens land use capability and crop yields worldwide. Understanding the mechanisms that protect soybeans from salt stress will help in the development of salt-stress tolerant leguminous plants. Here we initially analyzed the changes in malondialdehyde levels, the activities of superoxide dismutase and peroxidases, chlorophyll content, and Na(+)/K(+) ratios in leaves and roots from soybean seedlings treated with 200 mM NaCl at different time points. We found that the 200 mM NaCl treated for 12 h was optimal for undertaking a proteomic analysis on soybean seedlings. An iTRAQ-based proteomic approach was used to investigate the proteomes of soybean leaves and roots under salt treatment. These data are available via ProteomeXchange with the identifier PXD002851. In total, 278 and 440 proteins with significantly altered abundances were identified in leaves and roots of soybean, respectively. From these data, a total of 50 proteins were identified in the both tissues. These differentially expressed proteins (DEPs) were from 13 biological processes. Moreover, protein-protein interaction analysis revealed that proteins involved in metabolism, carbohydrate and energy metabolism, protein synthesis and redox homeostasis could be assigned to four high salt stress response networks. Furthermore, semi-quantitative RT-PCR analysis revealed that some of the proteins, such as a 14-3-3, MMK2, PP1, TRX-h, were also regulated by salt stress at the level of transcription. These results indicated that effective regulatory protein expression related to signaling, membrane and transport, stress defense and metabolism all played important roles in the short-term salt response of soybean seedlings."],"pubmed_title":["Comparative Proteomic Analysis of Soybean Leaves and Roots by iTRAQ Provides Insights into Response Mechanisms to Short-Term Salt Stress."],"pubmed_authors":["Ji Wei W, Cong Ru R, Li Sheng S, Li Rui R, Qin Zhiwei Z, Li Yanjun Y, Zhou Xiaolin X, Chen Sixue S, Li Jing J"],"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":["9.4."],"pubmed_title_synonyms":["Soybeans, reactivity, Salinity Stresses, Stress Response, Soybean, Phaseolus max, Bean, soybeans, Salinity Stress, Soy Beans, Salt, Salt Stresses, CG4216, stubby, Stress Reponse, Reponse, Salt Stress, soybean, ter, Soy Bean, cv. Wye, shortened, Salinity Stress Reponses, DmelCG4216, Salinity Stress Reaction., Stress Reaction, Bsg75C, Term, Reaction, Glycine max, responsivity, Salt Stress Reaction, Stress, proteomic analysis, Salt Stress Reactions, Salinity, Response, Salt Stress Response, Beans, Salt Stress Responses, Salinity Stress Reponse, response, Salinity Stress Reactions, short, Soy"],"name_synonyms":["exact)., exact), hoja (Spanish, 葉 (Japanese"],"pubmed_abstract_synonyms":["l(1)d norm-12, Trx-G, D14-3-3, Salinity Stresses, EG:17A9.1, BR_C, DMTRXIII, 14-3-3-e, Su(var)(3)6, Cobalt, Metabolisms, Mn-Superoxide Dismutase, DmelCG17870, Mn-Superoxide, 143E_DROME, DmTrxR, Metabolic Concepts, LUC7A, CG3864, 2Bc, growth and development, pp1alpha96A, CG32505, 4720, Malonaldehyde, Long Term, ter, solute:solute exchange, protein polypeptide chains, Lwr, l(1)2Bad, DmTrxR-1, l(1)2Bab, responsivity, br-Z1, ionic compounds, br-Z3, Salt Stress Response, Msal-1, FLW/PP1B, Cobalt Superoxide, Expenditure, Metabolism Concept, l(1)dn1, Cu-Superoxide, 4733, D14-3-3e, Phyllobilins, CG1459, l(2)07103, rbp, 1C5, Suvar(3)6, Grain, Su(Var)3-6, TrxR-1, CG9156, Soybean, K, catabolism, anon-WO02059370.52, PP4 19C, l(3)ck19, PP187B, FLW, BR, Salt, Tissue, par-5, Fe-Zn Superoxide Dismutase, Msal, composition, proteins, metabolic process resulting in cell growth, CG18339, inhibition of homeostatic process, sel, Salz, Br-C-Z3, salts, SID6-8061, HEL-S-66p, salt, Sodium Malondialdehyde, Bsg75C, Sprouted, Br, BRC-Z2, BRC-Z3, NR0A5, PPP4c, BRC-Z1, Salinity Stress Reponse, BRC-Z4, PP1c, DmPp1-87B, transcription from bacterial-type RNA polymerase promoter, DmelCG8651, 2G1, CG31884, DmelCG6593, single organism signaling, rdp, rds, tolerant, Iron Superoxide, ADF, PP1c 96A, anatomical protrusion, protein biosynthetic process, HS1, PP1alpha13C, Dismutase, 14-3-3e, land plants, sodium(I) cation, D8Wsu151e, metabolism resulting in cell growth, l(1)d.norm.1, Longterm Effect, Pp1-87Bb, integral to membrane, DmPpp4-19C, l(1)npr-1, l(1)npr1, Salinity Stress Reaction, Na(+), d14-3-3zeta, common salt, Plant Sprouts, PP4C, Term, Malonylaldehyde, protein formation, 4-3-3 zeta, secretion, PP1alpha-87B, Na+, PP1-87B, ck19, DmelCG2096, l(2)05487, Seeds, l(2)05486, 96A, PP1 13C, Stress Response, DmTR, Iron, craw, i56, ionic compound, content, CREAP-1, PP1 beta87b, DmPp1-96A, i105, 14-3-3, Seedling, Grains, higher plants, protein synthesis, Superoxide, gr, GR, Manganese Superoxide, PP13C, 1433epsilon, Salt Stress Reactions, CG1596, l(1)pp-2, l(1)pp-1, 31884, PP1beta, hLuc7A, Plant Sprout, dmtrxr-1, Effects, Gr, 2151, Processes, SASP, number, ingls, DmelCG32505, PP1 beta13c, Metabolic Processes, protein-containing complex, CG11511, 87B, dip4, pp1-87B, CG11514, PP1alpha[[1]], eps, CG2151, Salt Stress Reaction, Sprouted Seed, Fe Zn Superoxide Dismutase, Gene Products, Ubc 9, CG5650, DmPp1-13C, RGD1307981, Fe-Superoxide, BEST:GH05075, DmelCG3018, Longterm, Tissues, soybeans, l(3)s5452, Energy, Metabolic Concept, Hemocuprein, Dm-TrxR, Long-Term, Expenditures, EK3-5, PP-1alpha, Salt Stress, soybean, DmelCG4216, dis2m1, Stress Reaction, PP1 96A, Propanedial, Kochsalz, PAR-5, negative regulation of homeostatic process, DmelCG31884, Beans, l(1)PP1, l(1)pp1, BC032215, l(1)pp2, 14-3-3-epsilon, 549, Soy, Par-5, Su-var(3)6, DmelCG2151, Superoxide Dismutase, EG:123F11.1, DmelCG5650, CT24092, degradation, PP1 87B, Proteins, PP19C, compositionality, l(1)G0284a, Sprout, Trx, TRX, Pp-1alpha, Concept, Chlorophyll 740, 14-3-3omicron, native protein, Natriumchlorid, PP1beta-9C, Long Term Effects, chemical analysis, proteomic analysis, 14-3-3leo, PP-1G, 14-3-3-zeta, CRA, Sodium, PP1A87B, NaCl, ArPIKfyve, regulation of homeostatic process, metabolism, trx, Metabolic Phenomenon, Energy Expenditure, DTR, Sprouts, multicellular organism metabolic process, PP1alpha87B, Ovoperoxidase, Trxr1, postnatal growth, CG4216, Energy Expenditures, B130022O04Rik, Stress Reponse, Understanding, Longterm Effects, signalling, TrxR, Plant., Gene Proteins, signalling process, PP1alpha[[2]], AA959718, Dietary Sodium, Dmubc9, l(1)G0401, trxr-1, Glycine max, 14-3-3ZETA, Stress, structure, TRX1, D14-3-3zeta, BRC, dTrxR, LEO, Leo, Ag-Zn, reverse transcription polymerase chain reaction, CG3018, DmUbc9, Anabolism, PP, biochemical pathways, protein translation, DUbc9, Metabolic Process, single-organism developmental process, determination, postnatal development, Pp1, Bioenergetics, RT-PCR, Cu-Superoxide Dismutase, protein, leo, Reponse, BR-C, Tax1bp2, composed of, l(3)j3A2, Membrane Tissues, Readability, DTrx-2, halite, A18, br-C, CG8651, CG6593, PP1alpha96A, PP1, Concepts, Fe-Zn Superoxide, PP2, PP4, pp4, protein aggregate, PpX, BR-c, Br-C, Phenomenon, Effect, SODIUM ION, PP1 beta9c, Br-Z4, l(3)j6E7, CG31196, Malted Grain, l(1)G0318, DmTrx-2, de12, Soy Beans, membrane region, Salt Stresses, l(1)n34, BrC-Z1, plants, PPX, PP1beta9C, l(3)j14A6, cloruro sodico, 5.11, 13C, pp1-13C, Fe Superoxide Dismutase, CG2096, Reaction, su-var(3)6, signaling process, homeostasis, biotransformation, Cu Superoxide Dismutase, PP1 9C, Catabolism, Long-Term Effects, CG11491, Rg-bx, anon-WO03040301.120, Soybeans, Membrane Tissue, protein anabolism, rock salt, PP1B_DROME, ATL-derived factor, Process, CROP, Crop, BR-C Z1, anon-WO0118547.188, Manganese Superoxide Dismutase, membranous organ component, anon-WO0172774.141, uq, results, Soy Bean, shortened, positive regulation of homeostatic process, single-organism transport, Surface-associated sulphydryl protein, DmelTrx-2, DmelCG31196, hbl, Ag Zn Superoxide Dismutase, Seed, nrp1, TAX1BP2, l(2)02858, l(1)G0477, CG15305, membrane of organ, d14-3-3epsilon, Spalt, Phaseolus max, Pp1-96A, Plant, Fe-Superoxide Dismutase, DmPp1-9C, Mn-SOD, npr-1, SR3-9, DmelCG9156, natrii chloridum, 14-3-3EPSILON, cv. Wye, Salinity Stress Reponses, Energy Metabolisms, l(1)G0481, spine, bacterial transcription, npr, small molecule transport, Salinity Stress Reactions, short, Proteomes, Manganese, Pp1beta-9C, biological signaling, Cobalt Superoxide Dismutase, Mn SOD, Fe-Zn, l(1)G0379, l(1)G0018, DmelCG11491, Salinity Stress, Su(var)3-6, l(2)46Ee, D14-3-3epsilon, l(1)ts144, Gene, l(1)2Ba, l(1)2Bb, Z1, l(1)2Bc, Z2, Z3, Z4, presence, protrusion, PP1c 87B, sodium(1+), EG:25D2.1, polypeptide chain, Metabolism, integral component of membrane, nrp, Malondialdehyde, Chlorophylls, Br-C Z2, l(1)ts132, l(1)ts376, Malted, Ppl-87B, Metabolism Phenomena, Ag-Zn Superoxide, l(1)ESHS5, reactivity, IOPPP, l(1)G0154, l(3)j2B10, nprl, chlorure de sodium, stubby, Ubc-9, semi, l(2)01519, l(1)G0042, l(1)G0284, Pp1alpha-87B, l(1)2Bd, sels, l(3)87Bg, region of membrane, dmtrx-2, CG17870, npr1, Long-Term Effect, dPP4, Erythrocuprein, Autoregulation, sodium(1+) ion, PP-1, membrane, data, UBC9, Malted Grains, Ubc9, protein complex, trx-g, sales, OA48-18, ecs, trxI and trxII, R-bx, BrZ3, l(1)G0172, DmTrx, Metabolic Phenomena, Iron Superoxide Dismutase, development, Metabolism Concepts, count in organism, PP1 b9C, l(3)bx[v], FBgn0010602, natural protein, o.c.c., Ag-Zn Superoxide Dismutase, Protein, dUbc9, dUBC9, Phenomena, whole membrane, 14-3-30epsilon, protein biosynthesis, table salt, ubc9, TRDX, 14-3-3 epsilon, Sal, anon-WO03040301.185, anon-WO03040301.187, PP1 alpha96a, transmembrane, biodegradation, Metabolic, l(1)ts358, Bean, Salze, Membrane, Carbohydrate, Malonyldialdehyde, Bioenergetic, sal, Protein Gene Products, Su(Raf)3B, 2B5, single-organism metabolic process, activation of homeostatic process, Superoxide:superoxide oxidoreductase, Salinity, Sprouted Seeds, Response, PAR5, Salt Stress Responses, PP1alpha-13C, assay, response, PP1-13C, 14-3-3 zeta, growth, sodium cation, Mn Superoxide Dismutase, l(2)46CFe"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"Gmax - Leaf, NPSC (Jietal,frontplantsci,2016)","description":"abundance based on NPSC, Interaction consistency score: 9.4, Coverage: 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