{"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":["4932"],"full_dataset_link":["https://pax-db.org/dataset/4932/743986671"],"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":["Ubiquitination is a post-translational modification that signals multiple processes, including protein degradation, trafficking and DNA repair. Polyubiquitin accumulates globally during the oxidative stress response, and this has been mainly attributed to increased ubiquitin conjugation and perturbations in protein degradation. Here we show that the unconventional Lys63 (K63)-linked polyubiquitin accumulates in the yeast Saccharomyces cerevisiae in a highly sensitive and regulated manner as a result of exposure to peroxides. We demonstrate that hydrogen peroxide inhibits the deubiquitinating enzyme Ubp2, leading to accumulation of K63 conjugates assembled by the Rad6 ubiquitin conjugase and the Bre1 ubiquitin ligase. Using linkage-specific isolation methods and stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics, we identified >100 new K63-polyubiquitinated targets, which were substantially enriched in ribosomal proteins. Finally, we demonstrate that impairment of K63 ubiquitination during oxidative stress affects polysome stability and protein expression, rendering cells more sensitive to stress, and thereby reveal a new redox-regulatory role for this modification."],"pubmed_title":["K63 polyubiquitination is a new modulator of the oxidative stress response."],"pubmed_authors":["Silva Gustavo M GM, Finley Daniel D, Vogel Christine C"],"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":["DNA Oxidative, reactivity, Oxidative Injuries, Oxidative Stress, Injury, Anti-oxidative Stress, DNA Oxidative Damage, Antioxidative, Oxidative Cleavage, Antioxidative Stress, Nitrative Stress, responsivity., Cleavage, Oxidative DNA Damages, Anti-oxidative Stresses, Damage, Anti-oxidative, Nitro-Oxidative, Stresses, Oxidative Nitrative Stress, Oxidative Stress Injuries, Oxidative Stresses, Oxidative Nitrative, Anti oxidative Stress, Oxidative DNA, Oxidative, Oxidative DNA Damage, Stress Injury, Antioxidative Stresses, Oxidative and Nitrosative Stress, Oxidative Nitrative Stresses, Stress, Nitro-Oxidative Stress, Oxidative Cleavages, Oxidative Stress Injury, DNA Oxidative Damages, Nitro-Oxidative Stresses, DNA, response, Oxidative Injury, Nitro Oxidative Stress, DNA Damage, Oxidative Damages, Oxidative Damage"],"name_synonyms":["Koerper., organism, whole body, multi-cellular organism, whole organism, animal, body"],"pubmed_abstract_synonyms":["DNA Oxidative, Post Translational Amino Acid Modification, posttranslational modification, gamma Glutamyl Hydrolase, H2O2, polyubiquitin, Aminosaeure, Oxydol, Amino acid, Nitrative Stress, Ribosomal Protein, protein, Protein Processing, Damage, dihydrogen dioxide, Techniques, protein polypeptide chains, Carboxypeptidase G2, Carboxypeptidase G1, Oxidative DNA, Oxidative, Method, responsivity, Nitro-Oxidative Stress, Nitro-Oxidative Stresses, Oxidative Injury, protein aggregate, DNA Damage, Isotopically-Coded Affinity Tagging, Post-Translational Protein, increased, Oxidative Injuries, perhydrol, Ribosomal, posttranslational amino acid modification, ubiquitin hydrolase activity, Ubiquitylation, amino acids, High Mobility Protein 20, Hydroperoxide, Post-Translational, Moods, Oxidative Cleavage, Ubiquitin-related 1, Saccharomyes cerevisiae, Baker, proteins, procedures, Oxidative DNA Damages, Posttranslational Protein Processing, Saccharomyces uvarum var. melibiosus, ubiquitin C-terminal hydrolase, Protein Degradation, Anti-oxidative, allergic reaction, Ligase, APF-1, Oxidative Stress Injuries, Oxidative Stresses, Methodological Studies, Saccharomyces capensis, Pteroyl Polyglutamate Hydrolase, Baker's, Mycoderma cerevisiae, ubiquitination, brewer's yeast, Tagging, Stable Isotope Labeling, ubiquitin C-terminal hydrolase activity, Deubiquitinating, Post-Translational Modification, Degradations, anatomical protrusion, Aminokarbonsaeure, Modifications, Folate Conjugase, Procedure, CEP52, hBRE1, alpha-amino carboxylic acids, Baker's Yeasts, Conjugase, Folyl Poly-gamma-Glutamate Carboxypeptidase, Post Translational Modifications, Perhydrol, Saccharomyces diastaticus, Digestion, Oxidative and Nitrosative Stress, DNA Oxidative Damages, Ubiq, Culture Technique, Ubiquitin, Amino Acid, Acid, Yeast, BRE1, Superoxol, Rad6, RAD6, PTM, Hydrogen peroxide (H2O2), Amino acids, Deubiquitinases, Processing, Protein Digestions, Folate Hydrolyzing Enzyme, Human Ubiquitin, Methodological, Methodological Study, Nitro-Oxidative, Folacin Conjugase, GH, Saccharomyces cerevisiae (Desm.) Meyen ex E.C. Hansen, multicellular organismal protein catabolic process, Amino Acid Modification, spine, post-translational modification, Cell Cultures, Oxidative Stress Injury, Posttranslational Modifications, Acids, DNA, Brewer's Yeast, Posttranslational Modification, accessory, Oxidative Damage, HOOH, Oxidative Stress, Post-Translational Protein Modifications, Procedures, Peptidomics, Antioxidative, ubiquitinyl hydrolase 1 activity, Degradation, CG2013, Aminocarbonsaeure, number, Brewer's, Antioxidative Stress, baker's yeast, Gene, Synthetases, ATP Dependent Proteolysis Factor 1, Deubiquitinating Enzyme, Ubiquitin carboxyl extension protein 80, alpha-amino acid, Hydrogen Peroxide (H2O2), Isotope-Coded Affinity, protein-containing complex, supernumerary, presence, Saccharomyces italicus, deubiquitylase, 3.4.19.9, Posttranslational, protrusion, Stresses, Human, deubiquitinase activity, Oxidative Nitrative, PSO8, polypeptide chain, Stress Injury, sensitive, BRE1A, yeast, Post Translational Modification, DNA Damage Response, Studies, Gene Products, Oxidative Cleavages, HMG-20, Mood, Post-Translational Modifications, Isotopically-Coded Affinity, Cell Culture, sensitivity, Technique, Oxidative Damages, Post Translational, lager beer yeast, Modification, reactivity, Folylpolyglutamate Hydrolase, Injury, pheromone catabolism, Peroxide, posttranslational protein modification, Protein Degradations, Cell Culture Technique, S. cerevisiae, Protein Modifications, Post-Translational Amino Acid Modification, Study, UBP, 40S ribosomal protein S27a, S cerevisiae, Enzyme, Candida robusta, Anti oxidative Stress, Stable, Posttranslational Amino Acid Modification, Oxidative DNA Damage, Antioxidative Stresses, [OH(OH)], ubiquitin, Carboxypeptidase G, Isotope-Coded Affinity Tagging, Posttranslational Protein, 1883, protein tagging activity, Culture Techniques, Dhr6, Saccharomyces cerevisiae 'var. diastaticus', protein complex, Affects, Proteins, Post-Translational Protein Modification, Deubiquitinase, alpha-amino acids, Folyl Conjugate Synthetase, Anti-oxidative Stresses, Protein Digestion, Digestions, Labeling, Saccaromyces cerevisiae, Cell, Enzymes, Sccharomyces cerevisiae, Isotope, Oxidative Nitrative Stress, count in organism, DmelCG2013, Ubiquitin A-52 residue ribosomal protein fusion product 1, native protein, Proteolyses, natural protein, Ubiquitin-related 2, Stable Isotope, Oxidative Nitrative Stresses, Protein, Synthetase, sensitive., techniques, ATP-Dependent Proteolysis Factor 1, Protein Modification, Polysomes, UBC2, Isotope Coded Affinity Tagging, Polysome, Gamma-Glu-X carboxypeptidase, poly-, Saccharomyces oviformis, covalent modifier, pheromone catabolic process, Hydrogen, Anti-oxidative Stress, Folyl Polyglutamate Cleavage Enzyme, DNA Oxidative Damage, Post Translational Protein Processing, increased number, Isotope Labeling, Cleavage, Amino, Affinity Tagging, Isotopically-Coded, post-translational amino acid modification, UCH2, Protein Gene Products, present in greater numbers in organism, Gene Proteins, Post Translational Protein Modification, deubiquitinating enzyme, Polyribosome, 60S ribosomal protein L40, ligase, Stress, deubiquitinase, Post-Translational Protein Processing, Isotope-Coded, Ubiquitin-related, polyribosome, response, Baker's Yeast, Nitro Oxidative Stress, BcDNA:RE56673, Baker Yeast, methodology"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"S.cerevisiae - Whole organism, SC (Silvaetal,natstructmolbiol,2015)","description":"abundance based on Spectral counting, Interaction consistency score: 5.8, Coverage: 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