PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimary200OK0000ProteomicsChristian von Mering29760https://pax-db.org/dataset/29760/2450775963mering@imls.uzh.chUniversity of ZurichPAXDBFor the rescaling, the datasets are first parsed or processed such that the data reflect proportional abundances of whole protein molecules (i.e. proportionality to counts of complete, individual protein molecules, not to molecular weights, protein volumes, or digested peptides). In the case of spectral counting data protein. The proportional abundances are rescaled linearly to add up to one million; this means the abundance of each protein of interest is finally expressed in (parts per million,) relative to all other proteins in a sample. For a given protein abundance dataset, we then compute the absolute log abundance ratios of all pairs of proteins annotated to be functionally linked. The median of these absolute log abundance ratios represents an indirect quality metric: the closer it is to zero, the better (i.e. the more there is consistency between abundance values and functional annotations such as protein complexes or pathways). We then compute a background expectation for this metric, by permuting the abundance values in a given dataset randomly, and recomputing the median log abundance ratios. The permutation is repeated several times, yielding a distribution of medians. The actually observed median is then expressed as a Z-score distance to the random distribution ofmedians—this distance is termed the interaction consistency score.<h4>Background</h4>Grape cultivars and wines are distinguishable by their color, flavor and aroma profiles. Omic analyses (transcripts, proteins and metabolites) are powerful tools for assessing biochemical differences in biological systems.<h4>Results</h4>Berry skins of red- (Cabernet Sauvignon, Merlot, Pinot Noir) and white-skinned (Chardonnay, Semillon) wine grapes were harvested near optimum maturity (°Brix-to-titratable acidity ratio) from the same experimental vineyard. The cultivars were exposed to a mild, seasonal water-deficit treatment from fruit set until harvest in 2011. Identical sample aliquots were analyzed for transcripts by grapevine whole-genome oligonucleotide microarray and RNAseq technologies, proteins by nano-liquid chromatography-mass spectroscopy, and metabolites by gas chromatography-mass spectroscopy and liquid chromatography-mass spectroscopy. Principal components analysis of each of five Omic technologies showed similar results across cultivars in all Omic datasets. Comparison of the processed data of genes mapped in RNAseq and microarray data revealed a strong Pearson's correlation (0.80). The exclusion of probesets associated with genes with potential for cross-hybridization on the microarray improved the correlation to 0.93. The overall concordance of protein with transcript data was low with a Pearson's correlation of 0.27 and 0.24 for the RNAseq and microarray data, respectively. Integration of metabolite with protein and transcript data produced an expected model of phenylpropanoid biosynthesis, which distinguished red from white grapes, yet provided detail of individual cultivar differences. The mild water deficit treatment did not significantly alter the abundance of proteins or metabolites measured in the five cultivars, but did have a small effect on gene expression.<h4>Conclusions</h4>The five Omic technologies were consistent in distinguishing cultivar variation. There was high concordance between transcriptomic technologies, but generally protein abundance did not correlate well with transcript abundance. The integration of multiple high-throughput Omic datasets revealed complex biochemical variation amongst five cultivars of an ancient and economically important crop species.Five omic technologies are concordant in differentiating the biochemical characteristics of the berries of five grapevine (Vitis vinifera L.) cultivars.Ghan Ryan R, Van Sluyter Steven C SC, Hochberg Uri U, Degu Asfaw A, Hopper Daniel W DW, Tillet Richard L RL, Schlauch Karen A KA, Haynes Paul A PA, Fait Aaron A, Cramer Grant R GRAdd, 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, ratiowine grape, Grapes, Characteristics, Grape, Characteristic, Raisins, Vitis vinifera subsp. vinifera, Features, Raisin, Vitis vinifera., Featureepicarp, fruit peel, fruit skin, peel.IPP2A2, Materials, determination, LUC7A, BOUND WATER, protein, phenylpropanoid synthesis, Scents, HOH, 5730420M11Rik, Berries, Pod, protein polypeptide chains, primary metabolites, Abc8, Capsule, germacrene A synthase activity, protein aggregate, WMS, treatment, strong, SET, me75, Occidental, Gene Expressions, Genomes, TAF-I, Odorant, Plant Capsule, hypoplasia, Odors, proteins, D17Mit170, ecotype, T1, coenocarp (narrow), DmelCG4299, PA1, IGAAD, set, phenylpropanoid biosynthesis, DmelCG10574, sample, C16orf53, disease management, Plant Arils, RED, Red, Therapies, dihydridooxygen, Arils, dihydrogen oxide, GPHYSD2, SGS, Therapy, phapii, (+)-germacrene A synthase activity, AW413978, Vitis vinifera, CROP, Crop, aqua, Liquid Chromatography, StF-IT-1, white, Oligonucleotide, Tl3, Tl2, INSDC_feature:misc_RNA, results, HMG-CoAR, CSA2, ACMICD, H2O, European, species., Genetic Materials, cultivar, BXDC2, GAS, 6-trans-farnesyl-diphosphate diphosphate-lyase (germacrene-A-forming) activity, Scent, Genetic Material, Odor, Hydrogen Oxide, Caucasians, Pods, HLA-DR-associated protein II, DI-2, craw, I-2Dm, CREAP-1, Plant, hydrogen hydroxide, Capsules, Legume Pods, Raisins, CG4299, whole genome, MASS, exposed, Treatments, acqua, bxdc2, I-2PP1, TAF-IBETA, Material, syncarp (narrow), metabolites, microarray, White, Cistron, TAF-Ibeta, Wasser, i2pp2a, hLuc7A, Aromas, Plant Aril, Fruits, secondary metabolites, FBN, Gene, 2-trans, protein-containing complex, PHAPII, agua, Berry, Caucasian, resilient, polypeptide chain, reduced, Aril, ECTOL1, tough, Gene Products, Colors, Grapes, Low, Grape, tiny, RGD1307981, hYAK3-2, Genetic, ipp2a2, brix, 2pp2a, eau, Expressions, CG10574, BRIX, OCTD, extruding from, 2PP2A, taf-ibeta, Legume, dSET, dSet, Expression, Chromatographies, DYRK5, small, data, cou, protein complex, exits through, 6-trans-farnesyl-diphosphate diphosphate-lyase [(+)-germacrene-A-forming] activity, Proteins, OA48-18, Wines, igaad, Legume Pod, Aroma, (+)-(10R)-germacrene A synthase activity, Cistrons, Fragrance, group, strain, Lr, native protein, natural protein, I-2PP2A, Protein, Dm I-2, chemical analysis, I2PP2A, MFS1, CRA, background, Caucasoid, WMS2, ensemble, underdeveloped, metabolite, pH, REDK, sample population, introduction, Protein Gene Products, Gene Proteins, dSET/TAF-Ibeta, 2610030F17Rik, phenylpropanoid formation, Therapeutic, Whites, Raisin, SSKS, Plant Capsules, Bra, Fragrances, Treatment, phenylpropanoid anabolism, assay, [OH2], AA4077390falseVvinifera L. - Exocarp, NSAF (Ghanetal,bmcgenomics2015)abundance based on NSAF, Interaction consistency score: 4.9, Coverage: 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