PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering4113https://pax-db.org/dataset/4113/4093549508mering@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>Potato virus Y (PVY) is a major pathogen that causes substantial economic losses in worldwide potato production. Different potato cultivars differ in resistance to PVY, from severe susceptibility, through tolerance, to complete resistance. The aim of this study was to better define the mechanisms underlying tolerant responses of potato to infection by the particularly aggressive PVY(NTN) strain. We focused on the dynamics of the primary metabolism-related processes during PVY(NTN) infection.<h4>Results</h4>A comprehensive analysis of the dynamic changes in primary metabolism was performed, which included whole transcriptome analysis, nontargeted proteomics, and photosynthetic activity measurements in potato cv. Désirée and its transgenic counterpart depleted for accumulation of salicylic acid (NahG-Désirée). Faster multiplication of virus occurred in the NahG-Désirée, with these plants developing strong disease symptoms. We show that while the dynamics of responses at the transcriptional level are extensive and bimodal, this is only partially translated to the protein level, and to the final functional outcome. Photosynthesis-related genes are transiently induced before viral multiplication is detected and it is down-regulated later on. This is reflected as a deficiency of the photosynthetic apparatus at the onset of viral multiplication only. Interestingly, specific and constant up-regulation of some RuBisCO transcripts was detected in Désirée plants, which might be important, as these proteins have been shown to interact with viral proteins. In SA-deficient and more sensitive NahG-Désirée plants, consistent down-regulation of photosynthesis-related genes was detected. A constant reduction in the photochemical efficiency from the onset of viral multiplication was identified; in nontransgenic plants this decrease was only transient. The transient reduction in net photosynthetic rate occurred in both genotypes with the same timing, and coincided with changes in stomatal conductivity.<h4>Conclusions</h4>Down-regulation of photosynthesis-related gene expression and decreased photosynthetic activity is in line with other studies that have reported the effects of biotic stress on photosynthesis. Here, we additionally detected induction of light-reaction components in the early stages of PVY(NTN) infection of tolerant interaction. As some of these components have already been shown to interact with viral proteins, their overproduction might contribute to the absence of symptoms in cv. Désirée.Bimodal dynamics of primary metabolism-related responses in tolerant potato-Potato virus Y interaction.Stare Tjaša T, Ramšak Živa Ž, Blejec Andrej A, Stare Katja K, Turnšek Neža N, Weckwerth Wolfram W, Wienkoop Stefanie S, Vodnik Dominik D, Gruden Kristina KAdd, 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, ratioANTC, antp, ANT-C, Ant, Scx, MS/MS, BG:DS07700.1., MS2, Antp1, E430039A18Rik, DMANTPE1, Antp P1, Antp P2, CD156a, DmAntp, primary structure of sequence macromolecule, CG1028, CD156, Aus, Ns, DmelCG1028, Hu, AntP1, sequence, ANT-P, DRO15DC96Z, AntP, l(3)84Ba, ANTP, 3.4, tandem MSpotatoes, Potatoes, Potato Virus Ys, Solanum aracc-papa, tuberosum, Solanum tuberosum subsp. tuberosum, Solanum tuberosums, Potyviruses, Potato, PVY, potato virus Y PVY, potato, potato virus Y PVY-H, tuberosums, Ys, Solanum, primary metabolism, potato virus Y, Virus Ys, Potato Virus Y, Potato Virus.sequence, E430039A18Rik, CD156., exact), CD156a, hoja (Spanish, 葉 (Japanese, MS/MS, tandem MS, primary structure of sequence macromolecule, MS2Viridae, Ribulose Diphosphate Carboxylase, Materials, NetrinA, D430049E23Rik, Visible Light, 2 Hydroxybenzoic Acid, protein polypeptide chains, devices, Biological, hnu, symptoms, 1, Ribulosebiphosphate, Analysis, Profilings, Carboxylase Small-Subunit, Fs(3)Hor, Carbon Fixation, Biotic, Ribulose Biphosphate, Theory, Elkh, Utility Theories, Analyses, Nonmigrant, EK6, Economic Policies, Age of onset, proteins, Living Costs, SAP-2, Sap-2, NTef2, Transient, ecotype, allergic reaction, neuroendocrine tumour, Gene Expression Analysis, Solute carrier family 6 member 2, Vira, SLC6A5, Household Consumptions, Economic, Homo sapiens disease, Biphosphate Carboxylase-Oxygenase, Infections and Infestations, Physiological, screening, Elk, ELK, anatomical protrusion, Viral, Radiation, Indices, Index, 2-Hydroxybenzoic Acid, UNQ391/PRO726, Neuronally-expressed EPH-related tyrosine kinase, Potyviruses, land plants, Monitorings, Up-Regulation (Physiology), Ribulose, Physiological Stress Reaction, SAP2, Light, Calvin Benson Cycle, neuroendocrine neoplasm, Fs(3)Sz11, 5 Biphosphate Carboxylase, Small-Subunit, Economic Condition, LIGHT, Norepinephrine transporter, Utility Theory, Physiological Stress Reactions, Metabolic Stress Response, Macroeconomic, Ribulose Bisphosphate Carboxylase, Migrants and Transients, Salicylic, early T-cell activation antigen p60, Acid, Small Subunit, Stress Response, HVEML, Upregulation, Transcriptome Profilings, Consumer Price Indices, signs, Infection and Infestation, Calvin Benson Bassham Cycle, 5 Biphosphate Carboxylase Oxygenase, Home, 5 Bisphosphate Carboxylase Small Subunit, Condition, DmelCG18657, Solanum aracc-papa, higher plants, light quantum, Gene Expression Analyses, Material, CG2684, Ribulose 1, Animal Viruses, Migrants, potato virus Y PVY-H, AW488255, Policies, tuberosum, Peptidomics, Utility, Physiological Stress Reactivity, Reductive Pentose Phosphate Cycle, protein-containing complex, potato virus Y, Easterlin, Gene Expression Profilings, 5-Biphosphate Carboxylase, Ly113, Aim, AIM, mRNA Differential Displays, Abiotic Stress Reactions, Gene Expression Pattern Analysis, sensitive, Gene Products, disease or disorder, Physiological Stresses, Cek6, Biological Stresses, early activation antigen CD69, ERP, APUDoma, Erp, Animal Virus, findings., Receptor Up-Regulation, Lichtquant, o Hydroxybenzoic Acid, potato virus Y PVY, Microeconomic Factors, Transcriptomics, potato, Worker, clinical infection, Expressions, Monitoring, Genotypes, API6, ortho-Hydroxybenzoic Acid, Stress Reaction, Capital, C-type lectin domain family 2 member C, photon, Expression, TR2, NET, Net, Ribulose Diphosphate, C130099E04Rik, findings, Conditions, Proteins, disorders, 2-Hydroxybenzoic, inhibition of photosynthesis, Factor, MCMT, neuroendocrine tumor, CD258, net, Potato Virus Y, BL-AC/P26, Differential Display, Potato Virus Ys, Transcript Expression Analyses, native protein, Consumer Price Index, equipment, Consumer Price, Abiotic, chemical analysis, Strain, condition, Calvin-Benson Cycle, Ribulosebiphosphate Carboxylase, mRNA Differential Display, CXXC9, Gene Expression Monitoring, CT-2, mRNA, HVEM-L, 2-HYDROXYBENZOIC ACID, Ribulose Biphosphate Carboxylase Oxygenase, Carboxylase-Oxygenase, Differential Displays, Lds, Abiotic Stress Reaction, o-carboxyphenol, Gene Proteins, Genogroups, Photoradiations, Calvin Cycle, Nomads, Stress, General activity, 5-Bisphosphate Carboxylase Small-Subunit, netrin A, Severe, CLEC2C, apparatus, Activity, HSN1E, determination, 5-Bisphosphate, Solanum tuberosum subsp. tuberosum, Infestations and Infections, protein, Virus Ys, Photosynthetic Carbon Fixation, Productivity, Physiological Stress Response, Transcript Expression Analysis, diseases, Physiological Stress Responses, Gene Expression Monitorings, Virus, 3-Phospho-D-glycerate carboxy-lyase (dimerizing), pathogenesis, Abiotic Stress Responses, diseases and disorders, protein aggregate, Microeconomic, foton, human disease, DmelCG2684, appliances, Migrant Worker, Gene Expressions, Household Consumption, activation inducer molecule, plants, Ribulose-Bisphosphate, Calvin-Benson-Bassham, Ribulose Biphosphate Carboxylase, Ribulose Bisphosphate, Viral Gene Products, reaction, TNFSF14, Reaction, CT27014, Squatters, NET1, ortho Hydroxybenzoic Acid, TG, Calvin, Strains, Theories, netA, gamma, ortho-Hydroxybenzoic, Potato Virus, Metabolic Stress, Potatoes, 5-Biphosphate Carboxylase-Oxygenase, Home Economics, Biotic Stresses, Hypothesis, Potato, 9330129L11, Carboxylase, Macroeconomic Factors, 2-carboxyphenol, Economics, Gene Expression, o-Hydroxybenzoic acid, Physiological Stress, Household, Ribulose-Bisphosphate Carboxylase Large Subunit, Migrant, Diseases, Genetic Materials, EPH-like kinase 6, cultivar, Workers, o-hydroxybenzoic acid, tuberosums, Genetic Material, Visible Radiations, potatoes, ADCADN, Visible Radiation, Factors, Rubisco Small Subunit, UNQ203/PRO229, Plant, hEK6, Solanum, 5-Bisphosphate Carboxylase, early, Abiotic Stress, disease, Diphosphate Carboxylase, Easterlin Hypothesis, spine, Horka, Fs(3)Horka, Cistron, Viral Protein, Expression Analysis, Strains and Sprains, CD69, Ribulose-Bisphosphate Carboxylase Small Subunit, Remittances, other disease, Rubisco, Biological Stress, PVY, instruments, EA1, Gene, MLR-3, Ribulose Bisphosphate Carboxylase Small Subunit, Migrant Workers, protrusion, netrin, Metabolic Stresses, polypeptide chain, Hek6, Photosynthesis Dark Reactions, Cycle, Ribulose Bisphosphate Carboxylase Large Subunit, DmF2, Animal, Ys, Sprains, sensitivity, primary metabolism, o-Hydroxybenzoic, ENSMUSG00000074119, lod, study, Ribulose-1, Genetic, NTN, Viruses, Up Regulation, Transients, Tyrosine-protein kinase receptor EPH-2, o-Hydroxybenzoic Acid, Nonmigrants, causes, Transcript Expression, Transcriptome Analysis, Visible, Economic Conditions, 5-Biphosphate, non-neoplastic, Squatter, Infestation and Infection, leukocyte surface antigen Leu-23, 2.7.10.1, Etrp, causality, disorder, Calvin-Benson-Bassham Cycle, NAT1, Expression Analyses, Dark Reactions of Photosynthesis, Policy, Abiotic Stress Response, Economic Policy, Profiling, Transcriptome, protein complex, Photosynthetic, Sprain, DNMT, Photosynthesis Dark Reaction, EPH tyrosine kinase 2, Production, medical condition, Living Cost, Cistrons, Consumption, strain, viruses, Viral Gene Proteins, natural protein, Genogroup, Solanum tuberosums, Protein, Infection, Nomad, Biotic Stress, Metabolic Stress Responses, Zoophaginae, Radiations, Reactions, Transcriptome Profiling, Abiotic Stresses, Metabolic, Photoradiation, Age symptoms begin, CG18657, Transcriptome Analyses, LTg, Ribulose Biphosphate Carboxylase-Oxygenase, Protein Gene Products, Remittance, GP32/28, EPHT2, Carboxydismutase, Cost of Living, Response, assay, Calvin-Benson0falseStuberosum - Leaf, sequence+MS2 intensity (Stareetal,bmcgenomics2015)abundance based on sequence+MS2 intensity, Interaction consistency score: 3.4, Coverage: 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