{"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":["3702"],"full_dataset_link":["https://pax-db.org/dataset/3702/4072941425"],"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 growth and development are regulated by a tightly controlled interplay between cell division, cell expansion and cell differentiation during the entire plant life cycle from seed germination to maturity and seed propagation. To explore some of the underlying molecular mechanisms in more detail, we selected different aerial tissue types of the model plant Arabidopsis thaliana, namely rosette leaf, flower and silique/seed and performed proteomic, phosphoproteomic and transcriptomic analyses of sequential growth stages using tandem mass tag-based mass spectrometry and RNA sequencing. With this exploratory multi-omics dataset, development dynamics of photosynthetic tissues can be investigated from different angles. As expected, we found progressive global expression changes between growth stages for all three omics types and often but not always corresponding expression patterns for individual genes on transcript, protein and phosphorylation site level. The biggest difference between proteomic- and transcriptomic-based expression information could be observed for seed samples. Proteomic and transcriptomic data is available via ProteomeXchange and ArrayExpress with the respective identifiers PXD018814 and E-MTAB-7978."],"pubmed_title":["Proteomic and transcriptomic profiling of aerial organ development in Arabidopsis."],"pubmed_authors":["Mergner Julia J, Frejno Martin M, Messerer Maxim M, Lang Daniel D, Samaras Patroklos P, Wilhelm Mathias M, Mayer Klaus F X KFX, Schwechheimer Claus C, Kuster Bernhard B"],"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":["Arabidopsis, Arabidopsis thalianas, Cresses, A., A. thalianas, thalianas, Arabidopsis thaliana, Mouse-ear Cress, Cress, thaliana, Mouse ear, A. thaliana, Arabidopses, Mouse-ear Cresses, Mouse-ear, Cardaminopsis."],"name_synonyms":["rosette, leaf whorl."],"pubmed_abstract_synonyms":["Petals, Panomics, Plant Sepal, Materials, RNA Sequence Determination, single-organism developmental process, A., Sequence Determination, Pflanze, postnatal development, RNA Sequence, Phases, growth and development, protein, Stage, GRO:0005339, Life History, Divisions, Arabis thaliana, phosphorylation, viridiplantae, protein polypeptide chains, Arabidopsis thalianas, Sepal, Plant Bloom, A. thalianas, Plant Styles, Life Cycle, Blooms, Analysis, Plant Carpal, Bloom, Elaiosome, protein aggregate, WMS, Mass Spectrum Analysis, seed, M Phases, reference sample, Analyses, Determination, M, non-developmental growth of a unicellular organism, entire life cycle, Plant Ovary, Mouse-ear Cress, Tissue, aerial body, Plant Embryo, metabolic process resulting in cell growth, proteins, Plant Anther, Sequence Determinations, Pistil, Mouse-ear, Corolla, Division Phase, Corollas, Diaspores, flower, cellular growth, Arabidopses, GPHYSD2, SGS, Data Set, metabolism resulting in cell growth, Plant Anthers, Calyx, flower structure, A. thaliana, Cell Divisions, Pistils, Spectrum Analysis, INSDC_feature:misc_RNA, Determinations, ACMICD, Spectroscopy, C9orf7, Plant Corollas, Ovaries, non-developmental cell growth, Carpals, Arabidopsis thaliana (thale cress), Genetic Materials, Plant Blooms, Seed, Genetic Material, region, Anther, Multi Omics, Diaspore, growth pattern, Plant Corolla, non-developmental growth, life, Life Cycle Stage, methanol:5-hydroxybenzimidazolylcobamide Co-methyltransferase activity, Plant, Spectrometry, Integrative, History Stage, Plant Zygote, Filaments, Plant Calyx, MASS, Life Cycles, Arabidopsis, Plant Stigma, Material, Blossoms, Cistron, Anthers, methanol:corrinoid methyltransferase activity, Blossom, Stigma, lifespan, FBN, Gene, Calyxs, Spectrum Analyses, Plant Stigmas, protein-containing complex, Multi-Omics, Filament, aerial tissue, polypeptide chain, ECTOL1, Cycle, Stigmas, thalianas, Mass, Gene Products, silique, Life, Mass Spectroscopy, Styles, plantae, Cycles, floret (related), Genetic, Cell Division Phase, growth of cell, D9S2135, Cresses, entire lifespan, Flower Filaments, Zygote, MtaB., Cell Division, methyltransferase 1, Omics, Style, Division, Life History Stages, Sequencing, OCTD, thale-cress, Stages, RNA Sequence Analyses, Life History Stage, MT1, Plant Sepals, Zygotes, RNA Sequencing, site, Cress, Pan-Omics, Mouse ear, Plant Stamen, TAG, Differentiation, Stamens, Controlled, Sequence Analyses, Elaiosomes, Controlling, RNA, Carpal, Integrative-Omics, Arbisopsis thaliana, RNA Sequence Determinations, protein complex, Arabidopsis thaliana, Proteins, Ovary, Phosphorylations, Plant Carpals, GRO:0005250, Integrative Omics, Cistrons, FLOWER, Cell, development, cell expansion, methanol cobalamin methyltransferase activity, Plant Style, MS, native protein, natural protein, Embryos, Protein, Multi-Omic, methanol-corrinoid protein Co-methyltransferase., Pan Omics, MFS1, phosphorylation enrichment, M Phase, Plant Ovaries, Mass Spectrum Analyses, Flower Filament, WMS2, Differentiations, GRO:0005367, thale cress, mouse-ear cress, Embryo, covalent modifier, Mass Spectrum, Phase, methanol:5-hydroxybenzimidazolylcobamide methyltransferase activity, History Stages, Sepals, postnatal growth, thaliana, Plant Calyxs, Cell Differentiations, Plant Embryos, Mouse-ear Cresses, MT 1, Protein Gene Products, Flower, Gene Proteins, Stamen, Development and Growth, Plant Zygotes, Plant Stamens, Plant Petals, RNA Sequence Analysis, SSKS, Plant Petal, growth, Petal, pyrene (narrow)"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"A.thaliana - Rosette, SC (Mergneretal,scidata2020)","description":"abundance based on Spectral counting, Interaction consistency score: 10.2, Coverage: 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