{"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"},"statusCodeValue":200,"statusCode":"OK"}],"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/3708/2308287461"],"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":["Stomatal guard cell response to various stimuli is an important process that balances plant carbon dioxide (CO<sub>2</sub>) uptake and water transpiration. Elevated CO<sub>2</sub> induces stomatal closure, while low CO<sub>2</sub> promotes stomatal opening. The signaling process of elevated CO<sub>2</sub> induced stomatal closure has been extensively studied in recent years. However, the mechanism of low CO<sub>2</sub> induced stomatal opening is not fully understood. Here we report metabolomic and proteomic responses of <i>Brassica napus</i> guard cells to low CO<sub>2</sub> using hyphenated mass spectrometry technologies. A total of 411 metabolites and 1397 proteins were quantified in a time-course study of low CO<sub>2</sub> effects. Metabolites and proteins that exhibited significant changes are overrepresented in fatty acid metabolism, starch and sucrose metabolism, glycolysis and redox regulation. Concomitantly, multiple hormones that promote stomatal opening increased in response to low CO<sub>2</sub>. Interestingly, jasmonic acid precursors were diverted to a branch pathway of traumatic acid biosynthesis. These results indicate that the low CO<sub>2</sub> response is mediated by a complex crosstalk between different phytohormones."],"pubmed_title":["Metabolomics and Proteomics of <i>Brassica napus</i> Guard Cells in Response to Low CO<sub>2</sub>."],"pubmed_authors":["Geng Sisi S, Yu Bing B, Zhu Ning N, Dufresne Craig C, 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":["AT1G11140, Turnips, me75, cou, Rapeseeds, Peptidomics, mei-1794, Dub, rape, STRUBBELIG, Metabonomic, Metabonomics, Tl3, Tl2, rapeseeds, D17Mit170, Cell, T1, CG12298, STRUBBELIG-RECEPTOR FAMILY 9, SUB, Lr, DmelCG12298, Bra, SCRAMBLED, SRF9, Rapeseed, Low, oilseed rape, Metabolomic, Turnip, Rutabaga, T19D16.8, KIF20A, SCM, CG12298."],"name_synonyms":["occlusive cell (exact), exact), 孔辺細胞 (Japanese, MS/MS, MS2, sequence, E430039A18Rik, célula guardiana, CD156., stomatal guard cell, c&#233lula guardiana (Spanish, CD156a, 孔辺細胞, tandem MS, occlusive cell, primary structure of sequence macromolecule"],"pubmed_abstract_synonyms":["Pflanze, phytohormone, Amylum, Embden-Meyerhof, BOUND WATER, Progress Reports, Embden Meyerhof Parnas Pathway, Long Term, Social Controls, viridiplantae, HOH, SUB, Anhydride, primary metabolites, DmelCG12298, Carbonic, Summary Report, responsivity, SCRAMBLED, Dioxide, Embden-Meyerhof Pathway, Analysis, Effect, KIF20A, Summary Reports, Formal Social Controls, 2R)-3-oxo-2-(pent-2Z-enyl)-cyclopentaneacetic acid, multicellular organismal biosynthetic process, Mass Spectrum Analysis, increased, E290, single-organism biosynthetic process, me75, Progress Report, Analyses, Hormone Receptor, anabolism, rape, Pathways, proteins, elevated, D17Mit170, rapeseeds, T1, endocrine, Social, Progress, R-744, Starch, Field Reports, (1R, signaling process, Carbon, dihydridooxygen, dihydrogen oxide, Long-Term Effects, 2-dodecene-1, single organism signaling, Pathway, anatomical protrusion, Hormones, STRUBBELIG, aqua, Longterm Effect, anaerobic glycolysis, Receptor Agonists, Tl3, Embden-Meyerhof-Parnas, Tl2, Spectrum Analysis, results, E-290, Spectroscopy, Embden-Meyerhof-Parnas Pathway, H2O, Investigative Report, plant growth hormone, 2R)-3-oxo-2-(2Z)-2-penten-ylcyclopentanacetic acid, Rapeseed, sucrose metabolism, Phytohormone, Hydrogen Oxide, Amylomaize, Carbonic Anhydride, 2-{(1R, Field, Plant, hydrogen hydroxide, Spectrometry, Control, Jasmonate, Phytohormones, Controls, Embden-Meyerhof pathway, acqua, Report, glycolysis, spine, metabolites, plant growth factor, plant growth hormones, Plant Growth, Wasser, Regulation, Embden-Meyerhof Pathways, accessory, AT1G11140, Regulations, biological signaling, Carbon dioxide, bioformation, Effects, Amylomaize Starch, secondary metabolites, Gene, Growth Regulator, Growth Regulators, (-)-Jasmonic acid, biosynthesis, Spectrum Analyses, Cornstarch, supernumerary, CG12298, agua, protrusion, Hormone, Investigative, modified Embden-Meyerhof pathway, Mass, Gene Products, Plant Growth Regulator, Low, Agonists, Mass Spectroscopy, plantae, Plant Hormones, study, reactivity, hormones, jasmonate, CO2, lateral shoot, Plant Hormone, Longterm, formation, mei-1794, 7-epi-jasmonic acid, Hormone Receptor Agonists, eau, Long-Term, 2R)-3-oxo-2-[(Z)-pent-2-enyl]cyclopentyl}acetate, synthesis, SRF9, Long-Term Effect, Investigative Reports, Turnip, high elevation, axillary shoot, phytohormones., Regulators, cou, Embden Meyerhof Pathway, plant growth factors, Formal Social Control, Proteins, carbonic anhydride, [CO2], stomatal guard cell, Cell, STRUBBELIG-RECEPTOR FAMILY 9, uptake, Lr, MS, 12-dicarboxylic acid, plant hormones, native protein, Keoflo, Social Control, Research Reports, Protein, Long Term Effects, E 290, Rutabaga, Mass Spectrum Analyses, Mass Spectrum, Turnips, Rapeseeds, Regulator, increased number, 3-oxo-2-(2-pentenyl)cyclopentaneacetic acid, Dub, metabolite, (-)-jasmonic acid, Embden-Meyerhof-Parnas pathway, signalling, Longterm Effects, Protein Gene Products, Gene Proteins, present in greater numbers in organism, fatty acid metabolism, signalling process, Reports, Bra, regulation, response, oilseed rape, [OH2], Summary, T19D16.8, SCM, Field Report"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"Bnapus - Guard cell, sequence+MS2 intensity (Gengetal,frontmolbiosci2017)","description":"abundance based on sequence+MS2 intensity, Interaction consistency score: 6.2, Coverage: 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