{"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"},"statusCodeValue":200,"statusCode":"OK"}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Christian von Mering"],"species":["10116"],"full_dataset_link":["https://pax-db.org/dataset/10116/3976932592"],"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":["The human heart is capable of functioning for decades despite minimal cell turnover or regeneration, suggesting that molecular alterations help sustain heart function with age. However, identification of compensatory remodeling events in the aging heart remains elusive. We present the cardiac proteomes of young and old rhesus monkeys and rats, from which we show that certain age-associated remodeling events within the cardiomyocyte cytoskeleton are highly conserved and beneficial rather than deleterious. Targeted transcriptomic analysis in Drosophila confirmed conservation and implicated vinculin as a unique molecular regulator of cardiac function during aging. Cardiac-restricted vinculin overexpression reinforced the cortical cytoskeleton and enhanced myofilament organization, leading to improved contractility and hemodynamic stress tolerance in healthy and myosin-deficient fly hearts. Moreover, cardiac-specific vinculin overexpression increased median life span by more than 150% in flies. A broad array of potential therapeutic targets and regulators of age-associated modifications, specifically for vinculin, are presented. These findings suggest that the heart has molecular mechanisms to sustain performance and promote longevity, which may be assisted by therapeutic intervention to ameliorate the decline of function in aging patient hearts."],"pubmed_title":["Vinculin network-mediated cytoskeletal remodeling regulates contractile function in the aging heart."],"pubmed_authors":["Kaushik Gaurav G, Spenlehauer Alice A, Sessions Ayla O AO, Trujillo Adriana S AS, Fuhrmann Alexander A, Fu Zongming Z, Venkatraman Vidya V, Pohl Danielle D, Tuler Jeremy J, Wang Mingyi M, Lakatta Edward G EG, Ocorr Karen K, Bodmer Rolf R, Bernstein Sanford I SI, Van Eyk Jennifer E JE, Cammarato Anthony A, Engler Adam J AJ"],"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":["cardiac structure., metavinculin, Senescence, dorsal tube, vertebrate heart, alpha Vinculin, beta Vinculin, Herz, heart or heart like organ, adult heart, branchial heart, function, Hearts, Aging, Biological Aging, circulatory vessel, cardiac pump, chambered heart, Vinculin (Caenorhabditis elegans clone pRB9.1 protein moiety reduced), Biological, beta-Vinculin, alpha-Vinculin, heart, Isovinculin, cardium, VCL"],"name_synonyms":["lower chamber of heart., ventricle of heart, cardiac ventricle, ventricle, heart ventricle"],"pubmed_abstract_synonyms":["Heart, subgenus>, rhesus macaque, Heart Muscle Cells, Rat, fruit fly, Herz, Macaque, Microtrabecular, determination, Laboratory, Myocyte, adult heart, rhesus monkeys, Norway Rat, Non-Governmental Organizations, Aging, Norway Rats, CG11121, Cardiac Muscle, dmTAF[[II]]230, Actin Activated, circulatory vessel, rat, old, Cytoskeletons, Biological, symptoms, Chinese Rhesus Macaques, Norway rat, cardiomyocyte, Muscle Cell, Microtrabecular Lattice, Flies, Senescence, Life Span, Rhesus Macaques, Monkey, Man (Taxonomy), TFIID TAF250, Cytoplasmic Filament, cel, heart or heart like organ, Cytoskeletal, entire life cycle, Drosophilas, Length of Life, Myofilaments, Cardiac Myocytes, Fly, Myosin ATPase, Hemodynamic, cardiac structure, SO, SURGICAL AND MEDICAL PROCEDURES, Laboratory Rat, Biological Aging, Adenosinetriphosphatase, Hearts., Cardiomyocytes, Microtrabecular Lattices, Therapies, Isovinculin, MHC16, fruit flies, Organizations, So, Therapy, dorsal tube, vertebrate heart, screening, alpha Vinculin, dTAF[[II]]230, Lifespans, organisation, Modern, NMHC-II-C, TAF200, Actin Activated ATPase, Endogenous, Rhesus Monkeys, Rattus, striated muscle filament, TAFII-250, Procedure, TAF250/230, cardiocyte, chambered heart, TAFII250, Mus norvegicus, Rattus norwegicus, Vinculin (Caenorhabditis elegans clone pRB9.1 protein moiety reduced), RENBP, Cytoskeletal Filament, NMHC II-C, median, cardium, regulator, 1823, DFNA4, Drosophila <basidiomycete fungi>, True Flies, length of life, Nongovernmental, life, administrative structure, Myosin Adenosine Triphosphatase, fruit fly <Drosophila>, signs, Filaments, CG17603, TAF[[II]], rats, Treatments, human, Myofilament, AGE, Heart Muscle Cell, Endogenous Regeneration, Drosophila, Taf250, Patient, SR3-5, Drosophila Fruit Fly, Cells, heart muscle cell, Regeneration, microarray, Rhesus, Proteomes, TAF230, Drosophila <flies, Drosophila Fruit Flies, metavinculin, d230, Lattices, Drosophila Fallen, lifespan, human being, norvegicus, DFNA4A, Myosin Adenosinetriphosphatase, Macaca mulatta lasiotas, Cytoplasmic Filaments, branchial heart, organization and administration, dTAFII250, EfW1, Human, Intervention or Procedure, Filament, Rattus sp. strain Wistar, MYH17, Cardiac, myosin 1, Actin-Activated ATPase, Rats, Homo sapiens, dmTAF1, DmelCG11121, Taf230, beta-Vinculin, cardiac muscle fiber, Cytoskeletal Filaments, Non-Governmental, Rattus rattiscus, Man, VCL, TAF250, brown rat, Myofibril, Organization, Taf200, somda, dTAF[[II]]250, Rattus norvegicus, beta Vinculin, interventionDescription, cell, entire lifespan, True Fly, Interventional, Taf1p, Muscle Cells, man, Cytoplasmic, Drosophila Fruit, dTAF250, cardiac pump, ATPase, Non-Governmental Organization, Dipteras, myosin, Clients, alpha-Vinculin, Rhesus monkey, Cardiac Myocyte, organization, TAF, Chinese, Lifespan, Drl, Rattus norvegicus8, flies, Intervention Strategies, Rhesus Macaque, TAF[[II]]250, findings, Actomyosin Adenosinetriphosphatase, Life Spans, True, organizational structure, RnBP, Heart Muscle, GlcNAc 2-epimerase, l(3)84Ab, genus>, Hearts, BG:DS00004.13, function, Myosin, Client, Cell, Mdu, dTAF230, Chinese Rhesus Macaque, N-acetyl-D-glucosamine 2-epimerase, mda, p230, Laboratory Rats, cardiac muscle cell, heart, chemical analysis, Cercopithecus mulatta, TAF[[II]]250/230, TFIID, Cardiomyocyte, Nongovernmental Organizations, ami, administrative management, Intervention, Taf[[II]]250, Regenerations, PNMHH, MYOSIN, TAF[[II]]230, Adenosine Triphosphatase, med, rhesus macaques, TAF[II]250, patient, Cardiac Muscle Cells, Actomyosin ATPase, Macaca mulatta lasiota, Cardiac Muscle Cell, Fruit Flies, Actomyosin, Non Governmental Organizations, DmelCG17603, Therapeutic, Modern Man, cardiac myocyte, Lattice, renin-binding protein, organizational management, Fruit Fly, Treatment, Rhesus Monkey, Norway, assay, Nongovernmental Organization, Actin-Activated, TAF1, Gunn rats"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"R.norvegicus - Cardiac ventricle, normalized spectral counts (Kaushiketal,scitranslmed2015)","description":"abundance based on normalized spectral counts, Interaction consistency score: 7.5, Coverage: 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