PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering3702https://pax-db.org/dataset/3702/1326924861mering@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.Twenty-four-hour, circadian rhythms control many eukaryotic mRNA levels, whereas the levels of their more stable proteins are not expected to reflect the RNA rhythms, emphasizing the need to test the circadian regulation of protein abundance and modification. Here we present circadian proteomic and phosphoproteomic time series from Arabidopsis thaliana plants under constant light conditions, estimating that just 0.4% of quantified proteins but a much larger proportion of quantified phospho-sites were rhythmic. Approximately half of the rhythmic phospho-sites were most phosphorylated at subjective dawn, a pattern we term the "phospho-dawn." Members of the SnRK/CDPK family of protein kinases are candidate regulators. A CCA1-overexpressing line that disables the clock gene circuit lacked most circadian protein phosphorylation. However, the few phospho-sites that fluctuated despite CCA1-overexpression still tended to peak in abundance close to subjective dawn, suggesting that the canonical clock mechanism is necessary for most but perhaps not all protein phosphorylation rhythms. To test the potential functional relevance of our datasets, we conducted phosphomimetic experiments using the bifunctional enzyme fructose-6-phosphate-2-kinase/phosphatase (F2KP), as an example. The rhythmic phosphorylation of diverse protein targets is controlled by the clock gene circuit, implicating posttranslational mechanisms in the transmission of circadian timing information in plants.The Circadian Clock Gene Circuit Controls Protein and Phosphoprotein Rhythms in Arabidopsis thaliana.Krahmer Johanna J, Hindle Matthew M, Perby Laura K LK, Mogensen Helle K HK, Nielsen Tom H TH, Halliday Karen J KJ, van Ooijen Gerben G, Le Bihan Thierry T, Millar Andrew J AJAdd, 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, ratioMaterials, Arbisopsis thaliana, protein complex, A., Proteins, Arabidopsis thaliana, Gene, A. thaliana, protein, 5330400M04Rik, protein-containing complex, XClock, Cistrons, Arabis thaliana, clk, protein polypeptide chains, Arabidopsis thalianas, native protein, natural protein, polypeptide chain, A. thalianas, Protein, Gene Products, thalianas, Genetic Materials, Arabidopsis thaliana (thale cress), protein aggregate, Genetic Material, bHLHe8, thale cress, mouse-ear cress, Genetic, Cresses, Mouse-ear Cress, KAT13D, Arabidopsis., thaliana, INSDC_feature:gene, proteins, mKIAA0334, Phosphoprotein, Mouse-ear Cresses, Mouse-ear, phosphorylated protein, Protein Gene Products, Gene Proteins, Xclk, thale-cress, Material, Cistron, Cress, Prot/PhosRes+, Mouse ear, Arabidopsesrosette, leaf whorl.sodium salt, Networks, Ribonucleic, Materials, Kinship, land plants., Phosphatase, A., Visible Light, protein, Arabis thaliana, phosphorylation, prevention, Social Controls, ter, Phosphatases, protein polypeptide chains, Hydrolase, Arabidopsis thalianas, A. thalianas, hnu, Life Cycle, Kinase, protein aggregate, prevention and control, Non Polyadenylated, Formal Social Controls, foton, RNA Gene Products, Family Life Cycle, (alpha-D)-isomer, Kinship Network, reference sample, proportionality to, Polyadenylated Messenger, Mouse-ear Cress, KAT13D, proteins, plants, mKIAA0334, Phosphomonoesterases, Mouse-ear, MYB-RELATED DNA BINDING PROTEIN, Social, preventive measures, TNFSF14, h, Bsg75C, CCA1, TNT1, 2-(14)C-labeled, (beta-D)-isomer, Family Life Cycles, Arabidopses, phosphatase, gamma, close to, preventive therapy, Radiation, Polyadenylated, ribose nucleic acid, UNQ391/PRO726, land plants, (D)-isomer, ribonucleic acids, A. thaliana, Light, XClock, LIGHT, Term, Ribonukleinsaeure, pentosenucleic acids, Arabidopsis thaliana (thale cress), Genetic Materials, Ribonucleic acids, Filiation, Genetic Material, Polyadenylated Messenger RNA, Visible Radiations, Acid, Visible Radiation, Non Polyadenylated mRNA, protein_coding_transcript, HVEML, MtCCA, Time, disodium salt, proportionality, Control, Plant, barium (1:1) salt, rate, circadian clock associated 1, INSDC_feature:gene, Controls, Non-Polyadenylated mRNA, Life Cycles, Arabidopsis, higher plants, Phosphohydrolase, light quantum, Material, Phosphoric, HSNFRK, Biocatalyst, Cistron, Hydrolases, Regulation, Protein Kinase, Poly(A) RNA, Regulations, Family Member, Biocatalysts, barium salt, Gene, Network, 5330400M04Rik, Monoester Hydrolase, protein-containing complex, Ly113, protein amino acid phosphorylation, clk, polypeptide chain, Messenger, Gene Products, thalianas, bHLHe8, proportion, pattern, Genetic, Cresses, Research, distribution, Lichtquant, messenger RNA, Visible, ATP-protein phosphotransferase, Phosphoric Monoester Hydrolase, Non-Polyadenylated RNA, template RNA, thale-cress, DmelCG4216, Enzyme, photon, Cress, TR2, Mouse ear, Kinship Networks, Time Series, Family, Controlled, fructose-6-phosphate, Controlling, RNA, Family Research, 1-(14)C-labeled, Formal Social Control, Arbisopsis thaliana, protein complex, Proteins, Arabidopsis thaliana, Phosphorylations, Messenger RNA, RNS, Factor, CD258, Cistrons, Family Members, near to, Phosphomonoesterase, native protein, natural protein, Social Control, Poly(A)+ mRNA, yeast nucleic acid, Protein, INSDC_feature:mRNA, SIFD, phosphorylation enrichment, Polyadenylated RNA, magnesium (1:1) salt, F19D11.11, thale cress, Radiations, mouse-ear cress, ribonucleic acid, Phosphoric Monoester, Poly(A)+ RNA, mRNA, Poly(A) Tail, HVEM-L, Kinases, prophylaxis, Non Polyadenylated RNA, Photoradiation, Non-Polyadenylated, CG4216, thaliana, phosphoric monoester hydrolase activity, Ribonucleic Acid, Mouse-ear Cresses, LTg, Protein Gene Products, Phosphohydrolases, Gene Proteins, Xclk, Time Factor, Photoradiations, control, Families, approaches, vicinity of, quotient, calcium salt, regulation, Polyadenylated mRNA, Relatives0falseA.thaliana - Rosette, normalized abundance (Krahmeretal,molcellproteomics2022)abundance based on normalized abundance, Interaction consistency score: 6.7, Coverage: 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