{"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":["8030"],"full_dataset_link":["https://pax-db.org/dataset/8030/557577734"],"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":["<h4>Background</h4>Atlantic salmon production in Tasmania (Southern Australia) occurs near the upper limits of the species thermal tolerance. Summer water temperatures can average over 19 °C over several weeks and have negative effects on performance and health. Liver tissue exerts important metabolic functions in thermal adaptation. With the aim of identifying mechanisms underlying liver plasticity in response to chronic elevated temperature in Atlantic salmon, label-free shotgun proteomics was used to explore quantitative protein changes after 43 days of exposure to elevated temperature.<h4>Results</h4>A total of 276 proteins were differentially (adjusted p-value < 0.05) expressed between the control (15 °C) and elevated (21 °C) temperature treatments. As identified by Ingenuity Pathway Analysis (IPA), transcription and translation mechanisms, protein degradation via the proteasome, and cytoskeletal components were down-regulated at elevated temperature. In contrast, an up-regulated response was identified for NRF2-mediated oxidative stress, endoplasmic reticulum stress, and amino acid degradation. The proteome response was paralleled by reduced fish condition factor and hepato-somatic index at elevated temperature.<h4>Conclusions</h4>The present study provides new evidence of the interplay among different cellular machineries in a scenario of heat-induced energy deficit and oxidative stress, and refines present understanding of how Atlantic salmon cope with chronic exposure to temperature near the upper limits of thermal tolerance."],"pubmed_title":["Liver proteome response of pre-harvest Atlantic salmon following exposure to elevated temperature."],"pubmed_authors":["Nuez-Ortín Waldo G WG, Carter Chris G CG, Nichols Peter D PD, Cooke Ira R IR, Wilson Richard R"],"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":["PRE, CPD photolyase activity, PhrB photolyase activity, deoxyribonucleic cyclobutane dipyrimidine photolyase activity, total expressed protein, photoreactivating enzyme activity, pigmented epithelium, deoxyribodipyrimidine photolyase activity, jecur, MODIFIER OF SNC1, Salmon, retinal pigment, Atlantic salmon, responsivity, deoxyribonucleic photolyase activity, dipyrimidine photolyase (photosensitive), 3, stratum pigmentosa retinae, NUP96, Atlantic Salmon, epithelium, retinal pigment layer, Atlantic, reactivity, Atlantic Salmons, MOS3, RPE, deoxyribocyclobutadipyrimidine pyrimidine-lyase activity, PRECOCIOUS, photolyase activity, pigmented retina, iecur, F23A5.3, elevated, DNA cyclobutane dipyrimidine photolyase activity, 1758, SUPPRESSOR OF AUXIN RESISTANCE 3, p. pigmentosa retinae, Temperatures., Livers, phr A photolyase activity, DNA-photoreactivating enzyme, deoxyribonucleate pyrimidine dimer lyase (photosensitive), Salmons, response, high elevation, Proteomes, F23A5_3, Salmo salar Linnaeus"],"name_synonyms":["jecur, iecur., Livers"],"pubmed_abstract_synonyms":["protein translation, DNA Oxidative, l(3)LG9, HSN1E, determination, Sry-rDM33, Sry-rDM36, Nitrative Stress, BOUND WATER, protein, sci, Damage, l(3)j5E7, prevention, HOH, protein polypeptide chains, Readability, Oxidative DNA, diseases, Atlantic salmon, Oxidative, C230050L11, Multicatalytic Endopeptidase Complex, Dmel_CG13826, Endoplasmic Reticulum Stresses, type I, responsivity, Nitro-Oxidative Stress, TSK5, Sry-rDM23, HOW, How, NFT2, diseases and disorders, Nitro-Oxidative Stresses, protein aggregate, Oxidative Injury, prevention and control, DNA Damage, l(3)j5D5, Atlantic, Gm5098, 24B, average, portion of tissue, Atlantic Salmons, bony fishes, Oxidative Injuries, human disease, DM10, reference sample, Macropain, activation inducer molecule, Tissue, Oxidative Cleavage, hypoplasia, stru, iecur, proteins, RCH04A07, elevated, l(3)S053606, Oxidative DNA Damages, Fish, Proteasome Endopeptidase, 20S Proteasome, CG10293, free, Protein Degradation, Anti-oxidative, Sry-rDM10, preventive measures, l(3)j5B5, Oxidative Stress Injuries, Oxidative Stresses, dihydridooxygen, 26S proteasome, Homo sapiens disease, Dmel_CG17894, dihydrogen oxide, fish, FISH, transcription from bacterial-type RNA polymerase promoter, Sox70D, protein anabolism, 0904/17, Ito, preventive therapy, Degradations, Proteinase, protein biosynthetic process, Endopeptidase Complex, DM33, DM36, aqua, Normalcy, results, l(3)03921, NRF2A, H2O, Ingensin, ER stress, ray-finned fishes, DM23, Digestion, Oxidative and Nitrosative Stress, SZ1, ER, Cephalaspidomorphi, protein formation, tissue portion, simple tissue, DNA Oxidative Damages, Individual, AI413738, DmelCG43286, Hydrogen Oxide, Sry-rDM63, Christmas Island (Australia), proteasome, early T-cell activation antigen p60, ADCADN, Monorhina, UNQ203/PRO229, Endoplasmic Reticulum, Protein Digestions, hydrogen hydroxide, acqua, TKS5, Tks5, Temperatures., Nitro-Oxidative, disease, Health, multicellular organismal protein catabolic process, protein synthesis, label, bacterial transcription, Reticulum Stresses, Oxidative Stress Injury, anon-EST:Liang-2.39, Wasser, DNA, CD69, Proteomes, Salmo salar Linnaeus, Oxidative Damage, CG13826, other disease, Oxidative Stress, SOXB2.1, anon-WO0153538.7, anon-WO0153538.6, Canton and Enderbury Islands, Peptidomics, Antioxidative, fishes, P62, 2310014D11Rik, Degradation, number, Antioxidative Stress, EA1, Gene, MLR-3, protein-containing complex, Normalcies, presence, agua, jecur, Stresses, Agnatha, loD, amino acid degradation, Aim, Multicatalytic Proteinase, AIM, AA589508, DM63, Oxidative Nitrative, Sh3md1, polypeptide chain, reduced, E4TF1-60, Stress Injury, Gene Products, CG4566, Oxidative Cleavages, disease or disorder, ER Stress, Atlantic Salmon, tiny, CG5893, early activation antigen CD69, CNC, Cnc, Oxidative Damages, Normalities, reactivity, study, Injury, pheromone catabolism, l(3)s2612, Incontinentia pigmenti achromians, Complex, NRF2, Nrf2, eau, Protein Degradations, EG329070, 1758, non-neoplastic, API6, leukocyte surface antigen Leu-23, Multicatalytic Endopeptidase, Anti oxidative Stress, Oxidative DNA Damage, Multicatalytic, Antioxidative Stresses, DmelCG10293, C-type lectin domain family 2 member C, Macroxyproteinase, Chronic, disorder, species, high elevation, Controlled, small, Individual Health, DmelCG5893, Controlling, AI256723, Sox B2-1, Reticulum Stress, protein complex, clone 2.39, SH3MD1, Proteins, Sox70, DNMT, disorders, total expressed protein, medical condition, MCMT, Anti-oxidative Stresses, qkr, Protein Digestion, l(3)S090417, Digestions, Proteasome, Actinopterygi, BL-AC/P26, epsilon-COP, Incontinentia pigmenti type 1 (formerly), count in organism, BcDNA:RE05559, Oxidative Nitrative Stress, Salmon, Temperatures, native protein, natural protein, Proteolyses, SOX70D, Oxidative Nitrative Stresses, KH93F, Protein, chemical analysis, protein biosynthesis, condition, CG43286, background, CG17894, SOXDP, who, CXXC9, Hyperotreti, pheromone catabolic process, amino acid catabolism, Anti-oxidative Stress, CT-2, DNA Oxidative Damage, underdeveloped, Normality, Prosome, prophylaxis, ER Stresses, CG4578, 20S, CNC_DROME, Who/How, Understanding, Cleavage, introduction, Osteichthyes, Protein Gene Products, AI194320, Livers, Gene Proteins, Incontinentia pigmenti, cellular amino acid catabolic process, SOX70, HMI, 5134, Endoplasmic, GP32/28, control, Indexes, Stress, qkr[93F], E4TF1A, Salmons, assay, response, [OH2], multicatalytic endopeptidase, Nitro Oxidative Stress, amino acid breakdown, IPA, CLEC2C, formerly, proteasome endopeptidase complex"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"Ssalar - Liver, iBAQ (Nuez-ortinetal,bmcgenomics2018)","description":"abundance based on iBAQ, Interaction consistency score: 4.4, Coverage: 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