{"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":["3708"],"full_dataset_link":["https://pax-db.org/dataset/3708/1453244833"],"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":["Drought is one of the most widespread stresses leading to retardation of plant growth and development. We examined proteome changes of an important oil seed crop, canola (Brassica napus L.), under drought stress over a 14-day period. Using iTRAQ LC-MS/MS, we identified 1976 proteins expressed during drought stress. Among them, 417 proteins showed significant changes in abundance, and 136, 244, 286, and 213 proteins were differentially expressed in the third, seventh, 10th, and 14th day of stress, respectively. Functional analysis indicated that the number of proteins associated with metabolism, protein folding and degradation, and signaling decreased, while those related to energy (photosynthesis), protein synthesis, and stress and defense increased in response to drought stress. The seventh and 10th-day profiles were similar to each other but with more post-translational modifications (PTMs) at day 10. Interestingly, 181 proteins underwent PTMs; 49 of them were differentially changed in drought-stressed plants, and 33 were observed at the 10th day. Comparison of protein expression changes with those of gene transcription showed a positive correlation in B. napus, although different patterns between transcripts and proteins were observed at each time point. Under drought stress, most protein abundance changes may be attributed to gene transcription, and PTMs clearly contribute to protein diversity and functions."],"pubmed_title":["Comparative Proteomic Analysis of Brassica napus in Response to Drought Stress."],"pubmed_authors":["Koh Jin J, Chen Gang G, Yoo Mi-Jeong MJ, Zhu Ning N, Dufresne Daniel D, Erickson John E JE, Shao Hongbo H, Chen Sixue 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":["sequence, E430039A18Rik, CD156., CD156a, MS/MS, tandem MS, primary structure of sequence macromolecule, MS2"],"pubmed_title_synonyms":["rape, Turnips, Rapeseed, oilseed rape, Turnip, Rutabaga, Rapeseeds, rapeseeds, drought tolerance., proteomic analysis"],"name_synonyms":["sequence, E430039A18Rik, CD156., exact), CD156a, hoja (Spanish, 葉 (Japanese, MS/MS, tandem MS, primary structure of sequence macromolecule, MS2"],"pubmed_abstract_synonyms":["liquid chromatography tandem mass spectroscopy, biochemical pathways, single-organism catabolic process, multicellular organismal catabolic process, protein translation, Post Translational Amino Acid Modification, Metabolic Process, Materials, determination, Globular Protein Folding, Pflanze, postnatal development, Metabolic Concepts, LUC7A, growth and development, protein, beta-tubulin folding, GRO:0005339, Drought, Protein Processing, Photosynthetic Carbon Fixation, viridiplantae, protein polypeptide chains, canola, Concepts, cellular degradation, Metabolism Concept, Elaiosome, protein aggregate, Phenomenon, Carbon Fixation, Post-Translational Protein, seed, LCMSMS, Post-Translational, catabolism, rape, Plant Embryo, proteins, metabolic process resulting in cell growth, plants, Calvin-Benson-Bassham, Posttranslational Protein Processing, rapeseeds, Folding, chaperonin-mediated tubulin folding, Diaspores, signaling process, biotransformation, Calvin, 2610009E16Rik, drought tolerance, transcription from bacterial-type RNA polymerase promoter, Catabolism, time point, single organism signaling, LC-MS2, Post-Translational Modification, protein anabolism, protein biosynthetic process, Process, CROP, metabolism resulting in cell growth, land plants, Crop, Modifications, LC-MS/MS, Calvin Benson Cycle, chaperone activity, Menstruation, Post Translational Modifications, Globular Protein, co-chaperonin activity, protein formation, Genetic Materials, secretion, alpha-tubulin folding, Rapeseed, Seed, Protein Foldings, Genetic Material, ParaT, Diaspore, Brassica napus var. oleifera, breakdown, craw, Processing, CREAP-1, Plant, Plant Zygote, Calvin Benson Bassham Cycle, INSDC_feature:gene, co-chaperone activity, higher plants, Globular Protein Foldings, Amino Acid Modification, protein synthesis, Material, liquid chromatography-tandem mass spectroscopy, bacterial transcription, multichaperone pathway, Cistron, Posttranslational Modifications, Proteomes, Posttranslational Modification, hLuc7A, annual rape, biological signaling, Post-Translational Protein Modifications, Processes, Foldings, Gene, Reductive Pentose Phosphate Cycle, Metabolic Processes, protein-containing complex, cellular catabolism, LC-MS-MS, Posttranslational, polypeptide chain, Metabolism, chaperonin ATPase activity, LC-MSMS, Photosynthesis Dark Reactions, Cycle, Gene Products, Post Translational Modification, non-chaperonin molecular chaperone ATPase activity, glycoprotein-specific chaperone activity, Post-Translational Modifications, Metabolism Phenomena, Globular, RGD1307981, Post Translational, plantae, Modification, Genetic, breakdown of chemical, Metabolic Concept, Zygote, Brassica napus subsp. oleifera, Protein Modifications, Post-Translational Amino Acid Modification, Posttranslational Amino Acid Modification, Protein Folding, Zygotes, Posttranslational Protein, Calvin-Benson-Bassham Cycle, Brassica napus subsp. napus, Turnip, Dark Reactions of Photosynthesis, Gene., Elaiosomes, cellular breakdown, degradation, protein complex, Photosynthetic, OA48-18, Proteins, Photosynthesis Dark Reaction, total expressed protein, Post-Translational Protein Modification, Cistrons, Concept, Metabolic Phenomena, development, Metabolism Concepts, LC/MS/MS, native protein, Period, natural protein, Embryos, Protein, chemical analysis, Phenomena, protein biosynthesis, CRA, Calvin-Benson Cycle, Protein Modification, Rutabaga, metabolism, protein complex assembly, Metabolic Phenomenon, breakdown of molecule, Embryo, Turnips, multicellular organism metabolic process, biodegradation, Rapeseeds, Metabolic, Post Translational Protein Processing, postnatal growth, oil, Plant Embryos, signalling, Protein Gene Products, Gene Proteins, breakdown of substance, single-organism metabolic process, Post Translational Protein Modification, Development and Growth, signalling process, Plant Zygotes, Calvin Cycle, Post-Translational Protein Processing, liquid chromatography tandem mass spectrometry, assay, oilseed rape, Calvin-Benson, growth, pyrene (narrow), Anabolism"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"Bnapus - Leaf, sequence+MS2 intensity (Kohetal.,jproteomeres2015)","description":"abundance based on sequence+MS2 intensity, Interaction consistency score: 9.2, Coverage: 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