{"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":["9606"],"full_dataset_link":["https://pax-db.org/dataset/9606/1933621983"],"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 heart is a central human organ and its diseases are the leading cause of death worldwide, but an in-depth knowledge of the identity and quantity of its constituent proteins is still lacking. Here, we determine the healthy human heart proteome by measuring 16 anatomical regions and three major cardiac cell types by high-resolution mass spectrometry-based proteomics. From low microgram sample amounts, we quantify over 10,700 proteins in this high dynamic range tissue. We combine copy numbers per cell with protein organellar assignments to build a model of the heart proteome at the subcellular level. Analysis of cardiac fibroblasts identifies cellular receptors as potential cell surface markers. Application of our heart map to atrial fibrillation reveals individually distinct mitochondrial dysfunctions. The heart map is available at maxqb.biochem.mpg.de as a resource for future analyses of normal heart function and disease."],"pubmed_title":["Region and cell-type resolved quantitative proteomic map of the human heart."],"pubmed_authors":["Doll Sophia S, Dreßen Martina M, Geyer Philipp E PE, Itzhak Daniel N DN, Braun Christian C, Doppler Stefanie A SA, Meier Florian F, Deutsch Marcus-Andre MA, Lahm Harald H, Lange Rüdiger R, Krane Markus M, Mann Matthias M"],"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":["number, Platelets., count in organism, PLATEST, Estimated, presence, cardinality"],"pubmed_title_synonyms":["d230, human being, Herz, methionine aminopeptidase activity, number, A4, adult heart, branchial heart, dTAFII250, EfW1, presence, TYPE, Human, DAGA4, dmTAF[[II]]230, circulatory vessel, Homo sapiens, dmTAF1, Taf230, 2, MAM, SCG3, Man, familial adenomatous polyposis, MAP, peptidase M activity, TAF250, adenomas, cardiac structure., rabGAPLP, Taf200, L-methionine aminopeptidase activity, dTAF[[II]]250, Man (Taxonomy), TFIID TAF250, cel, cell, heart or heart like organ, familial adenomatous polyposis 2, RabGAP-5, Taf1p, man, autosomal recessive multiple colorectal adenomas, dTAF250, cardiac pump, RUSC3, site, TAF, dorsal tube, vertebrate heart, dTAF[[II]]230, TAF[[II]]250, MUTYH-Associated Polyposis, Modern, MYH-associated polyposis, TAF200, autosomal recessive familial adenomatous polyposis, Maps, l(3)84Ab, BG:DS00004.13, Hearts, TAFII-250, TAF250/230, Cell, LGMD2C, dTAF230, count in organism, TAFII250, chambered heart, p230, heart, sequence, TAF[[II]]250/230, TFIID, cardium, region, autosomal recessive, Taf[[II]]250, RUTBC3, TAF[[II]]230, DMDA1, TAF[II]250, MYH-Associated Polyposis, CG17603, TAF[[II]], primary structure of sequence macromolecule, human, RABGAP5, DmelCG17603, DMDA, Taf250, SR3-5, Modern Man, SCARMD2, multiple colorectal, MAP syndrome, TAF230, FAP2, TAF1, colorectal adenomatous polyposis"],"name_synonyms":["number, Platelets., count in organism, ventricle of heart, cardiac ventricle, ventricle, PLATEST, Estimated, heart ventricle, lower chamber of heart, presence, cardinality"],"pubmed_abstract_synonyms":["Herz, determination, methionine aminopeptidase activity, Persistent Atrial Fibrillation, adult heart, protein, element, cell associated, dmTAF[[II]]230, circulatory vessel, protein polypeptide chains, AF, Persistent Atrial, AAG, diseases, 2, diseases and disorders, Causes of Death, Atrial Fibrillations, Analysis, APNG, protein aggregate, peptidase M activity, organ, Mass Spectrum Analysis, adenomas, average, portion of tissue, rabGAPLP, human disease, me75, L-methionine aminopeptidase activity, Man (Taxonomy), TFIID TAF250, Analyses, cel, heart or heart like organ, Tissue, µg, RabGAP-5, proteins, Familial, Futurology, cardiac structure, D17Mit170, T1, scientific observation, RUSC3, sample, Homo sapiens disease, Predictions and Projections, dorsal tube, vertebrate heart, dTAF[[II]]230, PIG11, Atrial fibrillation (disorder), Paroxysmal, Modern, Paroxysmal Atrial Fibrillations, MYH-associated polyposis, TAF200, ug, autosomal recessive familial adenomatous polyposis, atrial fibrillation, Maps, Familial Atrial, TAFII-250, TAF250/230, Tl3, PIG16, Tl2, Spectrum Analysis, Spectroscopy, chambered heart, TAFII250, ATP synthase D chain, Diseases, tissue portion, simple tissue, cardium, autosomal recessive, RUTBC3, Epistemology, Mitochondrial, anpg, Death Cause, Spectrometry, Paroxysmal Atrial, CG17603, TAF[[II]], human, RABGAP5, disease, Taf250, AF - Atrial fibrillation, SR3-5, multiple colorectal, Death Causes, medical condition., Familial Atrial Fibrillation, Atrial, cell bound, ANPG, Proteomes, TAF230, Fibroblast, other disease, d230, human being, Peptidomics, Fibrillation, branchial heart, Gene, dTAFII250, Spectrum Analyses, protein-containing complex, EfW1, mitochondrial, Atrial Fibrillation, Human, Persistent Atrial Fibrillations, Homo sapiens, polypeptide chain, dmTAF1, Taf230, Mid1, MID1, Gene Products, Mass, disease or disorder, Projections and Predictions, Low, Man, familial adenomatous polyposis, Mass Spectroscopy, MAP, TAF250, Taf200, ADPG, dTAF[[II]]250, Auricular Fibrillations, cell, familial adenomatous polyposis 2, Taf1p, man, non-neoplastic, autosomal recessive multiple colorectal adenomas, dTAF250, cardiac pump, anatomical unit, body organ, disorder, TAF, measuring, TAF[[II]]250, cou, MUTYH-Associated Polyposis, protein complex, Proteins, disorders, MDG, total expressed protein, l(3)84Ab, Hearts, medical condition, BG:DS00004.13, function, Cell, dTAF230, MS, Lr, native protein, natural protein, p230, Familial Atrial Fibrillations, heart, Protein, chemical analysis, TAF[[II]]250/230, condition, TFIID, Mass Spectrum Analyses, Paroxysmal Atrial Fibrillation, Taf[[II]]250, Mass Spectrum, CRA36.1, Auricular Fibrillation, TAF[[II]]230, Fibrillations, distinct, TAF[II]250, MYH-Associated Polyposis, A-fib, sample population, Protein Gene Products, AFib, Gene Proteins, DmelCG17603, Auricular, Persistent, Modern Man, Bra, atrial fibrillation (disease), MAP syndrome, assay, Future, FAP2, TAF1, colorectal adenomatous polyposis"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"H.sapiens - Cardiac ventricle, copy number estimated from proteomic ruler (Dolletal,natcomm2017)","description":"abundance based on copy number estimated from proteomic ruler, Interaction consistency score: 15.6, Coverage: 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