{"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":["4097"],"full_dataset_link":["https://pax-db.org/dataset/4097/1689759783"],"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":["Recently, we published a set of tobacco lines expressing the <i>Daucus carota</i> (carrot) <i>DcLCYB1</i> gene with accelerated development, increased carotenoid content, photosynthetic efficiency, and yield. Because of this development, <i>DcLCYB1</i> expression might be of general interest in crop species as a strategy to accelerate development and increase biomass production under field conditions. However, to follow this path, a better understanding of the molecular basis of this phenotype is essential. Here, we combine OMICs (RNAseq, proteomics, and metabolomics) approaches to advance our understanding of the broader effect of <i>LCYB</i> expression on the tobacco transcriptome and metabolism. Upon <i>DcLCYB1</i> expression, the tobacco transcriptome (~2,000 genes), proteome (~700 proteins), and metabolome (26 metabolites) showed a high number of changes in the genes involved in metabolic processes related to cell wall, lipids, glycolysis, and secondary metabolism. Gene and protein networks revealed clusters of interacting genes and proteins mainly involved in ribosome and RNA metabolism and translation. In addition, abiotic stress-related genes and proteins were mainly upregulated in the transgenic lines. This was well in line with an enhanced stress (high light, salt, and H<sub>2</sub>O<sub>2</sub>) tolerance response in all the transgenic lines compared with the wild type. Altogether, our results show an extended and coordinated response beyond the chloroplast (nucleus and cytosol) at the transcriptome, proteome, and metabolome levels, supporting enhanced plant growth under normal and stress conditions. This final evidence completes the set of benefits conferred by the expression of the <i>DcLCYB1</i> gene, making it a very promising bioengineering tool to generate super crops."],"pubmed_title":["A Multi-OMICs Approach Sheds Light on the Higher Yield Phenotype and Enhanced Abiotic Stress Tolerance in Tobacco Lines Expressing the Carrot <i>lycopene</i> β<i>-cyclase1</i> Gene."],"pubmed_authors":["Moreno Juan C JC, Martinez-Jaime Silvia S, Kosmacz Monika M, Sokolowska Ewelina M EM, Schulz Philipp P, Fischer Axel A, Luzarowska Urszula U, Havaux Michel M, Skirycz Aleksandra A"],"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"],"pubmed_title_synonyms":["Panomics, 9-cis, Materials, Biological Stress, Physiological Stress Reactivity, Gene, Visible Light, Ly113, Metabolic Stresses, Multi-Omics, Physiological Stress Response, Pro-Lycopene, Abiotic Stress Reactions, Biological, Physiological Stress Responses, hnu, Lycopene, Physiological Stresses, Abiotic Stress Responses, All trans Lycopene, Biological Stresses, foton, All-trans-Lycopene, Biotic, Carrot, 7'-cis, LYC-O-MATO, Genetic, Lichtquant, LYC O MATO, (7-cis, Pro Lycopene, Omics, Visible, Daucus, 9'-cis)-isomer -, TNFSF14, Stress Reaction, psi-Carotene, Reaction, photon, Pan-Omics, Carrots, TR2, gamma, Physiological, Abiotic Stress Response, Metabolic Stress, Integrative-Omics, Radiation, Biotic Stresses, UNQ391/PRO726, Nicotiana tabacum var. Samsun, Physiological Stress Reaction, Light, Integrative Omics, tobacco, CD258, Cistrons, Physiological Stress, LIGHT, Abiotic, Nicotania tabacum, Multi-Omic, Physiological Stress Reactions, (cis)-isomer, Pan Omics, Biotic Stress, Metabolic Stress Responses, Genetic Materials, Metabolic Stress Response, American tobacco, (13-cis)-isomer, Visible Radiations, Radiations, Multi Omics, Visible Radiation, Stress Response, psi, HVEML, Reactions, Abiotic Stresses, Metabolic, HVEM-L, Photoradiation, Integrative, INSDC_feature:gene, Abiotic Stress Reaction, Prolycopene, LTg, Abiotic Stress, Phenotypes, light quantum, Photoradiations, Material, common tobacco, Stress, Response, Cistron, Genetic Material., LYCOMATO"],"name_synonyms":["exact)., exact), hoja (Spanish, 葉 (Japanese"],"pubmed_abstract_synonyms":["Materials, Metabolisms, Metabolic Concepts, LUC7A, A4, Embden-Meyerhof, ribosomal RNA, growth and development, Metabonomics, Visible Light, Profiles, secondary metabolite metabolism, 5730420M11Rik, protein polypeptide chains, DmelCG12298, Biological, hnu, ionic compounds, Msal-1, SCRAMBLED, Metabolism Concept, Biotic, average, SET, Theory, Utility Theories, catabolism, developmental field, Salt, Economic Policies, Pathways, Msal, metabolic process resulting in cell growth, proteins, Living Costs, sel, Salz, Signatures, salts, DmelCG4299, set, salt, Expression Signature, Household Consumptions, Economic, Physiological, Pathway, Tetraterpene Derivatives, protein biosynthetic process, Radiation, Indices, Index, UNQ391/PRO726, metabolism resulting in cell growth, STRUBBELIG, CG3424, anaerobic glycolysis, Physiological Stress Reaction, Light, Embden-Meyerhof-Parnas, RNA metabolism, Embden-Meyerhof-Parnas Pathway, Economic Condition, common salt, LIGHT, Utility Theory, Expression Signatures, protein formation, Physiological Stress Reactions, secretion, Metabolic Stress Response, Macroeconomic, secondary metabolism, Expression Profile, Stress Response, HLA-DR-associated protein II, HVEML, DI-2, craw, ionic compound, I-2Dm, CREAP-1, Consumer Price Indices, INSDC_feature:gene, Home, I-2PP1, Condition, Phenotypes, light quantum, TAF-IBETA, glycolysis, protein synthesis, Bio, Material, common tobacco, Cytosols, TAF-Ibeta, Embden-Meyerhof Pathways, hLuc7A, secondary metabolite metabolic process, lipids, Policies, Peptidomics, Processes, Utility, Physiological Stress Reactivity, secondary metabolites, Kern, Metabolic Processes, protein-containing complex, Easterlin, Ly113, organ field, Abiotic Stress Reactions, Gene Products, Physiological Stresses, field, Biological Stresses, MAM, nucleo atomico, Metabolic Profile, Bio-Engineering, RGD1307981, plantae, Lichtquant, Profile, mei-1794, 2pp2a, Metabolic Concept, Microeconomic Factors, CG10574, 2PP2A, Stress Reaction, Capital, Kochsalz, dSET, dSet, photon, species, TR2, Carotenoid, degradation, Conditions, Proteins, Factor, CD258, Cell, Concept, whole transcriptome, Secondary Metabolisms, Carotene, native protein, Consumer Price Index, Natriumchlorid, I-2PP2A, Consumer Price, Abiotic, Nicotania tabacum, Dm I-2, Gene Expression Signatures, CRA, American tobacco, NaCl, metabolism, Metabolic Phenomenon, free ribosome, Wall, Ribosome, multicellular organism metabolic process, DMDA1, ensemble, HVEM-L, Dub, postnatal growth, metabolite, B130022O04Rik, nucleus of neuraxis, Understanding, Abiotic Stress Reaction, neuraxis nucleus, Gene Proteins, Photoradiations, Biomasses, Gene Expression Profiles, Dietary Sodium, Stress, Anabolism, biochemical pathways, protein translation, IPP2A2, Metabolic Process, single-organism developmental process, Bio engineerings., Pflanze, postnatal development, Bioengineerings, Metabonomic, Gene Expression Profile, protein, Embden Meyerhof Parnas Pathway, Atomkern, viridiplantae, Productivity, Physiological Stress Response, SUB, Readability, DmelCG3424, primary metabolites, halite, Physiological Stress Responses, horsetail nucleus, Concepts, Abiotic Stress Responses, Embden-Meyerhof Pathway, protein aggregate, Phenomenon, Microeconomic, foton, KIF20A, Metabolic Profiles, Cell Walls, Carrot, neuronal nucleus, nucleus atomi, carotenoids, TAF-I, Household Consumption, carrots, Daucus, Chloroplast, cloruro sodico, IGAAD, TNFSF14, DmelCG10574, Derivatives, Reaction, Transcriptomes, biotransformation, TG, Theories, Catabolism, gamma, phapii, Metabolic Stress, protein anabolism, rock salt, Home Economics, Biotic Stresses, Process, Hypothesis, CROP, Crop, Expression Profiles, StF-IT-1, future organ, tobacco, Bio engineering, Macroeconomic Factors, Economics, engineerings, Gene Expression, Physiological Stress, Household, engineering, Lipid, Genetic Materials, cell nucleus, Genetic Material, Transcriptome Profiles, Visible Radiations, Visible Radiation, Factors, Spalt, growth pattern, non-developmental growth, Plant, CG4299, natrii chloridum, Embden-Meyerhof pathway, Abiotic Stress, pth, DMDA, Easterlin Hypothesis, metabolites, Cistron, i2pp2a, anon-WO0118547.271, Proteomes, Remittances, AT1G11140, noyau atomique, Transcriptome Profile, Biological Stress, Gene, TYPE, PHAPII, CG12298, Metabolic Stresses, DAGA4, polypeptide chain, Metabolism, modified Embden-Meyerhof pathway, Metabolomic, Metabolism Phenomena, SCG3, anon-WO0118547.370, Walls, nuclei, Biological Engineering, Genetic, Metabolomes, nucleus of CNS, nucleo, noyau, ipp2a2, chlorure de sodium, Visible, Economic Conditions, Etioplast, nucleus, taf-ibeta, sels, Tetraterpenes, Carrots, SRF9, Policy, Abiotic Stress Response, Economic Policy, carotenes and carotenoids, Transcriptome, Embden Meyerhof Pathway, protein complex, Carotenes, sales, OA48-18, igaad, Queen Anne's lace, Nicotiana tabacum var. Samsun, total expressed protein, Production, Etioplasts, Living Cost, Cistrons, group, LGMD2C, Consumption, Metabolic Phenomena, STRUBBELIG-RECEPTOR FAMILY 9, development, Metabolism Concepts, natural protein, nervous system nucleus, Protein, I2PP2A, Phenomena, protein biosynthesis, Biotic Stress, Metabolic Stress Responses, table salt, Gene Expression Signature, membrane bound ribosome, Sal, Radiations, Reactions, biodegradation, Abiotic Stresses, Metabolic, Photoradiation, Engineering, Salze, Embden-Meyerhof-Parnas pathway, LTg, sal, Protein Gene Products, Secondary, dSET/TAF-Ibeta, 2610030F17Rik, Tetraterpene, single-organism metabolic process, Remittance, Cost of Living, SCARMD2, Response, Signature, AA407739, growth, T19D16.8, SCM"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"Ntabacum - Leaf, iBAQ (Morenoetal,frontplantsci2021)","description":"abundance based on iBAQ, Interaction consistency score: 12.6, Coverage: 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