PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimary200OK0000ProteomicsChristian von Mering8030https://pax-db.org/dataset/8030/587673189mering@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.Marine oils are important to human nutrition as the major source of docosahexaenoic acid (DHA), a key omega-3 long-chain (≥C20) polyunsaturated fatty acid (n-3 LC-PUFA) that is low or lacking in terrestrial plant or animal oils. The inclusion of fish oil as main source of n-3 LC-PUFA in aquafeeds is mostly limited by the increasing price and decreasing availability. Fish oil replacement with cheaper terrestrial plant and animal oils has considerably reduced the content of n-3 LC-PUFA in flesh of farmed Atlantic salmon. Novel DHA-enriched oils with high alpha-linolenic acid (ALA) content will be available from transgenic oilseeds plants in the near future as an alternative for dietary fish oil replacement in aquafeeds. As a preliminary validation, we formulated an oil blend (TOFX) with high DHA and ALA content using tuna oil (TO) high in DHA and the flaxseed oil (FX) high in ALA, and assessed its ability to achieve fish oil-like n-3 LC-PUFA tissue composition in Atlantic salmon smolts. We applied proteomics as an exploratory approach to understand the effects of nutritional changes on the fish liver. Comparisons were made between fish fed a fish oil-based diet (FO) and a commercial-like oil blend diet (fish oil + poultry oil, FOPO) over 89 days. Growth and feed efficiency ratio were lower on the TOFX diet. Fish muscle concentration of n-3 LC-PUFA was significantly higher for TOFX than for FOPO fish, but not higher than for FO fish, while retention efficiency of n-3 LC-PUFA was promoted by TOFX relative to FO. Proteomics analysis revealed an oxidative stress response indicative of the main adaptive physiological mechanism in TOFX fish. While specific dietary fatty acid concentrations and balances and antioxidant supplementation may need further attention, the use of an oil with a high content of DHA and ALA can enhance tissue deposition of n-3 LC-PUFA in relation to a commercially used oil blend.Preliminary Validation of a High Docosahexaenoic Acid (DHA) and α-Linolenic Acid (ALA) Dietary Oil Blend: Tissue Fatty Acid Composition and Liver Proteome Response in Atlantic Salmon (Salmo salar) Smolts.Nuez-Ortín Waldo G WG, Carter Chris G CG, Wilson Richard R, Cooke Ira I, Nichols Peter D PDAdd, 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, ratioDHEA, 9-cis, Saturated Fatty, acido graso, 7Z, Esterified Fatty Acids, acidos grasos, 19-docosahexaenoic acid, Docosahexaenoic acid, 22:6-4, PC80, (9, linolenic acid, docosahexaenoic acids, linolenic acids, 10Z, Linolenic Acid, (E, 10, jecur, 12, Docosahexenoic Acids, Potassium Salt, 13, 15, 15-octadecatrienoic acid, 16, Intrarosa, cis-Delta(9, docosa-4, 19, acides gras, Atlantic salmon, responsivity, Diets, (Z, Saturated Fatty Acids, 3, 4, EP770, Esterified Fatty Acid, 6, Atlantic Salmon, 7, 9, 19-(Z, DHA, Atlantic, Esterified, A, portion of tissue, reactivity, Fatty Acids, Atlantic Salmons, E, Docosahexaenoic Acid (All-Z Isomer), 22:6(n-3), Esterified Fatty, Aliphatic, Tissue, 19-hexaenoic acid, Doconexent, iecur, 19-Isomer, 12-cis, 18-Isomer, alanina, 3beta-Hydroxyandrost-5-en-17-one, 12Z, Z, Lithium Salt, Docosahexaenoic Acid, 1758, Z)-Isomer, 15-Octadecatrienoic acid, Aliphatic Acids, Docosahexaenoic Acid Dimer (All-Z Isomer), Cerium Salt, (9Z, DmelCG3525, 15)-octadecatrienoic acid, Linolensaeure, all-cis-9, Docosahexenoic, all-cis-4, ALA, 13Z, Linolenate, 19-(All-Z-Isomer), Saturated, 19Z)-Docosahexaenoic acid, 19-HEXAENOIC ACID, Tin(2+) Salt, EtnK, Docosahexaenoate, Atlantic., 3beta-hydroxyandrost-5-en-17-one, total expressed protein, ala, Fettsaeuren, Prasterone, DOCOSA-4, cis-9, 15-cis-octadecatrienoic acid, 2-Aminopropionic acid, Fettsaeure, C18:3, Salmon, all-cis-DHA, E)-Isomer, alpha-Linolenic Acid, Magnesium Salt, tissue portion, Ammonium Salt, simple tissue, Cesium Salt, 3-BETA-HYDROXY-5-ANDROSTEN-17-ONE, Dehydroisoandrosterone, Acid, alpha Linolenic Acid, Fatty Acid, Saturated Fatty Acid, 15)-linolenic acid, cis, (4Z, Dietary, Z)-9, oil, Aliphatic Acid, 16Z, E-Isomer), 2-Aminopropanoic acid, Alanin, acide gras, Docosahexaenoic, RE10142, CG3525, 19-Docosahexaenoic acid, Livers, Zinc Salt, fatty acids, Sodium Salt, 15Z)-Octadecatrienoic acid, RH11, cervonic acid, Acids, Salmons, response, Proteomes, Calcium Salt, Salmo salar Linnaeus, Z)-jecur, iecur., LiversDHEA, acido graso, Unsaturated, acidos grasos, l(3)LG9, 22:6-4, PC80, growth and development, Docosahexenoic Acids, docosa-4, Oxidative DNA, C230050L11, Oxidative, responsivity, TSK5, 3, 4, Nitro-Oxidative Stresses, 6, 7, 9, 19-(Z, DNA Damage, DHA, Atlantic, Esterified, Animalia, A, Poultries, bony fishes, E, DM10, Docosahexaenoic Acid (All-Z Isomer), Esterified Fatty, Tissue, Oxidative Cleavage, composition, 18-Isomer, 3beta-Hydroxyandrost-5-en-17-one, Z, Lithium Salt, D17Mit170, Social, Aliphatic Acids, Oxidative Stresses, all-cis-9, all-cis-4, 19-(All-Z-Isomer), DM33, DM36, animalia, land plants, Antioxidants, Docosahexaenoate, Endogenous, Fettsaeuren, Tl3, Tl2, alpha-lecithin cholesterol acyltransferase deficiency, DmIKKgamma, all-cis-DHA, oil., DM23, dIKK, Cephalaspidomorphi, Magnesium Salt, simple tissue, DNA Oxidative Damages, AI413738, Acid, Fatty Acid, whole organism, Saturated Fatty Acid, 15)-linolenic acid, cis, (4Z, content, IKK-gamma, Z)-9, E-Isomer), CG3525, human, Nitro-Oxidative, Zinc Salt, fatty acids, Sodium Salt, higher plants, 15Z)-Octadecatrienoic acid, Koerper, Acids, Domestic Fowls, DNA, Salmo salar Linnaeus, Oxidative Damage, Saturated Fatty, LCATA deficiency, Esterified Fatty Acids, multi-cellular organism, Peptidomics, Docosahexaenoic acid, Antioxidative, fishes, Endogenous Antioxidant, 2310014D11Rik, (9, antioxydant, docosahexaenoic acids, dIKK-gamma, (E, Human, Agnatha, jecur, DM63, DmIKK-gamma, Diets, (Z, Projections and Predictions, Atlantic Salmon, CG5893, Man, Oxidative Damages, Unsaturated Fatty Acid, Partial LCAT deficiency, dyslipoproteinemic corneal dystrophy, plantae, Fatty Acids, Injury, Tissues, 12-cis, man, Docosahexaenoic Acid, Fowl, Z)-Isomer, (9Z, Antioxidative Stresses, Antioxidant Activity, ALA, DmelCG5893, AI256723, Sox B2-1, cou, body, SH3MD1, Polyunsaturated Fatty, Sox70, whole body, ala, compositionality, Anti-oxidative Stresses, Prasterone, Actinopterygi, 2-Aminopropionic acid, IKKgamma, Fettsaeure, Salmon, Lr, Linseed, E)-Isomer, Oxidative Nitrative Stresses, Antioxidant Effect, chemical analysis, feed, Oil, Focus of Attention, 3-BETA-HYDROXY-5-ANDROSTEN-17-ONE, Dehydroisoandrosterone, Anti-oxidative Stress, underdeveloped, DNA Oxidative Damage, storage, Dmikkgamma, alpha-LCAT deficiency, postnatal growth, oil, Mental Concentration, Alanin, muscle, acide gras, CG16910, SOX70, structure, Stress, Bra, Salmons, sequestering, Muscle Tissue, Calcium Salt, 9-cis, DNA Oxidative, Anti Oxidants, Tunas, Activity, determination, Pflanze, postnatal development, Sry-rDM33, Sry-rDM36, linolenic acid, Nitrative Stress, Domestic Fowl, Unsaturated Fatty Acids, 10Z, composed of, Linolenic Acid, Damage, 10, viridiplantae, Productivity, 12, 13, 15, 16, Intrarosa, Polyunsaturated Fatty Acid, Tier, cis-Delta(9, 19, Atlantic salmon, Nitro-Oxidative Stress, Sry-rDM23, Saturated Fatty Acids, Esterified Fatty Acid, Oxidative Injury, animal, Polyunsaturated, IKKg, KEY, Key, Gm5098, portion of tissue, Atlantic Salmons, Anti Oxidant, Oxidative Injuries, me75, Muscle Tissues, Man (Taxonomy), availability, 22:6(n-3), long, Aliphatic, 19-hexaenoic acid, hypoplasia, Doconexent, iecur, alanina, plants, Futurology, Domestic, Fish, 12Z, Oxidative DNA Damages, T1, Anti-oxidative, retention, Sry-rDM10, 15-Octadecatrienoic acid, Oxidative Stress Injuries, DmelCG3525, Antioxidant, 15)-octadecatrienoic acid, Anti-Oxidant Effect, fish-eye disease, Docosahexenoic, TG, fish, 13Z, FISH, Sox70D, Predictions and Projections, Flaxseed, 19-HEXAENOIC ACID, EtnK, Modern, Attention Focus, DOCOSA-4, cis-9, Anti-Oxidants, organism, Attention, ray-finned fishes, alpha-Linolenic Acid, Oxidative and Nitrosative Stress, Kenny, tissue portion, Ammonium Salt, Fowls, Sry-rDM63, Monorhina, antioxidants, growth pattern, non-developmental growth, Plant, Aliphatic Acid, 16Z, TKS5, Tks5, muscle element, 19-Docosahexaenoic acid, Endogenous Antioxidants, DmelCG16910, RH11, cervonic acid, Oxidative Stress Injury, Z)-, Mental, 7Z, Oxidative Stress, SOXB2.1, human being, 19-docosahexaenoic acid, antoxidant, Antioxidative Stress, Selective, loD, Stresses, Potassium Salt, alpha-lecithin:cholesterol acyltransferase deficiency, 15-octadecatrienoic acid, AA589508, Sh3md1, Oxidative Nitrative, Homo sapiens, reduced, acides gras, Stress Injury, Anti-Oxidant, Oxidative Cleavages, EP770, Low, dmIKKgamma, Animal, tiny, Anti-Oxidant Effects, IKK[[gamma]], reactivity, Linseed oil, Unsaturated Fatty, 19-Isomer, metazoa, EG329070, 1758, FED, Docosahexaenoic Acid Dimer (All-Z Isomer), IKK, Anti oxidative Stress, Social Attention, Cerium Salt, Oxidative DNA Damage, Concentration, musculus, Linolenate, small, Saturated, 19Z)-Docosahexaenoic acid, Tin(2+) Salt, 3beta-hydroxyandrost-5-en-17-one, Muscle, Anti Oxidant Effect, 15-cis-octadecatrienoic acid, development, Oxidative Nitrative Stress, Selective Attention, SOX70D, Metazoa, Cesium Salt, SOXDP, Hyperotreti, Anti Oxidant Effects, alpha Linolenic Acid, Dietary, 2-Aminopropanoic acid, Docosahexaenoic, Cleavage, RE10142, Osteichthyes, Livers, Antioxidant Effects, concentration, Polyunsaturated Fatty Acids, Modern Man, assay, response, Future, Nitro Oxidative Stress, growth, Flaxseed Oil0falseSsalar - Liver, iBAQ (Nuez-ortinetal,plosone2016)abundance based on iBAQ, Interaction consistency score: 4.8, Coverage: 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