{"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":["10090"],"full_dataset_link":["https://pax-db.org/dataset/10090/1153777653"],"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":["Protein stability is a major regulatory principle of protein function and cellular homeostasis. Despite limited understanding on mechanisms, disruption of protein turnover is widely implicated in diverse pathologies from heart failure to neurodegenerations. Information on global protein dynamics therefore has the potential to expand the depth and scope of disease phenotyping and therapeutic strategies. Using an integrated platform of metabolic labeling, high-resolution mass spectrometry and computational analysis, we report here a comprehensive dataset of the in vivo half-life of 3,228 and the expression of 8,064 cardiac proteins, quantified under healthy and hypertrophic conditions across six mouse genetic strains commonly employed in biomedical research. We anticipate these data will aid in understanding key mitochondrial and metabolic pathways in heart diseases, and further serve as a reference for methodology development in dynamics studies in multiple organ systems."],"pubmed_title":["A large dataset of protein dynamics in the mammalian heart proteome."],"pubmed_authors":["Lau Edward E, Cao Quan Q, Ng Dominic C M DC, Bleakley Brian J BJ, Dincer T Umut TU, Bot Brian M BM, Wang Ding D, Liem David A DA, Lam Maggie P Y MP, Ge Junbo J, Ping Peipei P"],"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"],"description_synonyms":["38.1."],"pubmed_title_synonyms":["big, dorsal tube, vertebrate heart, Herz, Data Set, gyltl1b-b, protein complex, Proteins, Mbp1, total expressed protein, Gene, adult heart, branchial heart, protein, Hearts, protein-containing complex, froggy, Gyltl1a, circulatory vessel, large, protein polypeptide chains, chambered heart, native protein, natural protein, polypeptide chain, MDDGA6, mKIAA0609, Protein, heart, Proteomes., Gene Products, cardium, protein aggregate, myd, KIAA0609, fg, gyltl1b, heart or heart like organ, MDDGB6, mdc1d, expanded, Mbp-1, LARGE, proteins, cardiac structure, Protein Gene Products, BPFD#36, Gene Proteins, MDC1D, cardiac pump, enr, enlarged, great"],"name_synonyms":["cardiac structure., dorsal tube, vertebrate heart, circulatory vessel, cardiac pump, chambered heart, Herz, heart or heart like organ, musculus, heart, adult heart, branchial heart, cardium, muscle, Hearts, muscle element"],"pubmed_abstract_synonyms":["Heart, Metabolic Networks, Networks, single-organism developmental process, determination, Chronic heart failure, Laboratory, Mus domesticus, postnatal development, Heart failure NOS, growth and development, protein, Progress Reports, House Mouse, heart trouble, Heart failure, protein polypeptide chains, Readability, Donor Artificial Insemination, unspecified, cardiac insufficiency, diseases, Summary Report, CDA2, Myocardial Failure, Heart Disease, diseases and disorders, Analysis, protein aggregate, cardiac dysfunction, Congestive, Summary Reports, IKKg, Donor Artificial, KEY, Key, Mass Spectrum Analysis, organ, human disease, Decompensation, Analyses, Progress Report, Pathways, Swiss Mice, proteins, procedures, Heart failure NOS (disorder), genetic, Progress, Field Reports, Halflifes, Pathologies, Half Life, Therapies, Medicine, Homo sapiens disease, Strains, insufficiency, house mouse, CHF, Therapy, Heart Disorder, Cardiac Failure, Pathway, Data Set, Cardiac failures, Cardiac Disorder, Heart: [weak] or [failure NOS], mouse, familial, Metabolic Network, Heart failure (disorder), Spectrum Analysis, mice C57BL/6xCBA/CaJ hybrid, heart disorder, Spectroscopy, Left Sided, Congestive Heart Failure, DmIKKgamma, Experimental, Half-Lifes, Investigative Report, ATP synthase D chain, dIKK, Diseases, Kenny, Heterologous Insemination, failure, Weak heart, Right Sided, Left-Sided, Mus musculus, Mitochondrial, heart/pericardial trouble, Left Sided Heart Failure, mice, Field, Swiss Mouse, IKK-gamma, Spectrometry, Left-Sided Heart Failure, Treatments, domesticus, disease, Artificial Insemination, Report, DmelCG16910, Protein Stabilities, Mouse, inherited genetic, heart disease or disorder, heart/pericardial disease, Strains and Sprains, Right-Sided, other disease, disorder of heart/pericardium, Cardiac Diseases, Gene, Heart Diseases, Network, Spectrum Analyses, protein-containing complex, mitochondrial, AID, Aid, dIKK-gamma, Cardiac Disease, Biomedical, disease of heart, Stability, Cardiac, disease or disorder of heart, Cardiac failure, Investigative, polypeptide chain, House, heart/pericardial disorder, DmIKK-gamma, Medical Research, Gene Products, Mass, disease or disorder, Mus musculus domesticus, element., dmIKKgamma, IKK[[gamma]], Mice, Sprains, Medical, Mass Spectroscopy, aid, Insemination, Research, Swiss, heart/pericardial disease or disorder, labeling, disorder of heart, non-neoplastic, Halflife, CARDIAC DIS, IKK, anatomical unit, HEL-S-284, body organ, Investigational Medicine, disorder, HIGM2, Right-Sided Heart Failure, HEART DIS, Right Sided Heart Failure, Investigative Reports, constitutitional genetic, Heterologous, data, Disease, protein complex, Proteins, Sprain, disorders, function, medical condition, Heart Failure, Cardiac Disorders, Mus muscaris, Human Donor, Stabilities, heart failure, development, Investigative Medicine, IKKgamma, MS, native protein, natural protein, Mus, Protein, heart, chemical analysis, Research Reports, Strain, condition, Donor, techniques, Mass Spectrum Analyses, Investigational, Metabolic Pathways, cardiac failure, Artificial, Mass Spectrum, Heart Disorders, Metabolic, Arp2, Dmikkgamma, ARP2, Experimental Medicine, postnatal growth, House Mice, heart disease, Understanding, CG16910, macromolecular stability of protein, Heart Decompensation, Laboratory Mice, Protein Gene Products, Gene Proteins, Cardiac insufficiency, Therapeutic, Reports, cardiac disease, Metabolic Pathway, Treatment, assay, Summary, hereditary, growth, Laboratory Mouse, Field Report, methodology"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"M.musculus - Heart, NSAF (Lauetal,scidata2016)","description":"abundance based on NSAF, Interaction consistency score: 38.1, Coverage: 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