PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering10090https://pax-db.org/dataset/10090/3284560666mering@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.Aging promotes lung function decline and susceptibility to chronic lung diseases, which are the third leading cause of death worldwide. Here, we use single cell transcriptomics and mass spectrometry-based proteomics to quantify changes in cellular activity states across 30 cell types and chart the lung proteome of young and old mice. We show that aging leads to increased transcriptional noise, indicating deregulated epigenetic control. We observe cell type-specific effects of aging, uncovering increased cholesterol biosynthesis in type-2 pneumocytes and lipofibroblasts and altered relative frequency of airway epithelial cells as hallmarks of lung aging. Proteomic profiling reveals extracellular matrix remodeling in old mice, including increased collagen IV and XVI and decreased Fraser syndrome complex proteins and collagen XIV. Computational integration of the aging proteome with the single cell transcriptomes predicts the cellular source of regulated proteins and creates an unbiased reference map of the aging lung.An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics.Angelidis Ilias I, Simon Lukas M LM, Fernandez Isis E IE, Strunz Maximilian M, Mayr Christoph H CH, Greiffo Flavia R FR, Tsitsiridis George G, Ansari Meshal M, Graf Elisabeth E, Strom Tim-Matthias TM, Nagendran Monica M, Desai Tushar T, Eickelberg Oliver O, Mann Matthias M, Theis Fabian J FJ, Schiller Herbert B HBAdd, 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, ratioPeptidomics., Profiling, dTAF[[II]]230, TAF[[II]]250, d230, Transcriptome, pulmo, lung parenchyma, TAF200, Monitorings, l(3)84Ab, Gene, dTAFII250, BG:DS00004.13, Aging, TAFII-250, TAF250/230, EfW1, Cell, dTAF230, Gene Expression Profilings, dmTAF[[II]]230, Gene Expression, Differential Display, Transcript Expression Analysis, TAFII250, mRNA Differential Displays, Transcript Expression Analyses, Gene Expression Pattern Analysis, dmTAF1, Biological, parenchyma of lung, Taf230, p230, lung, Gene Expression Monitorings, TAF[[II]]250/230, tissue portion, TFIID, simple tissue, Analysis, Profilings, neoplasm, mRNA Differential Display, neoplasms, TAF250, Taf[[II]]250, Senescence, portion of tissue, Gene Expression Monitoring, Taf200, dTAF[[II]]250, TAF[[II]]230, TFIID TAF250, Transcriptome Profiling, Analyses, mRNA, cel, cell, Transcriptome Profilings, C1, Tissue, Taf1p, Transcriptomics, TAF[II]250, Differential Displays, Transcript Expression, Transcriptome Analysis, CG17603, TAF[[II]], Transcriptome Analyses, Monitoring, Atlases, dTAF250, Biological Aging, Gene Expression Analysis, DmelCG17603, Gene Expression Analyses, pulmonary, Taf250, SR3-5, Lungs, Expression Analysis, TAF, Expression Analyses, TAF230, TAF1lung, parenchyma of lung., lung parenchyma, Lungs, muscle, pulmo, pulmonary, neoplasm, neoplasms, musculus, muscle elementCollagens, Epithelial Cell, Activity, lung disease, methionine aminopeptidase activity, Laboratory, LUNG DIS, Mus domesticus, A4, Gene Expression Profile, FRASS, CASP-14, lung disorder, Profiles, Aging, Glandular, House Mouse, pulmonary disorder, prevention, CG11121, dmTAF[[II]]230, Transcript Expression Analysis, old, Biological, parenchyma of lung, Type-II, Gene Expression Monitorings, 2, Causes of Death, Analysis, Profilings, Extracellular Matrices, Zyderm, prevention and control, peptidase M activity, Mass Spectrum Analysis, adenomas, Senescence, rabGAPLP, L-methionine aminopeptidase activity, disorder of lung, TFIID TAF250, Charts, reference sample, Analyses, cel, Microfibril Collagen Hemostat, RabGAP-5, Swiss Mice, Adenomatous Epithelial, proteins, SO, Signatures, Epigenomic, pulmonary disorders, preventive measures, Biological Aging, Gene Expression Analysis, Alveolar, Type-II Pneumocytes, collagen, Expression Signature, RUSC3, Collagen Fleece, cholesterol anabolism, Transcriptomes, Collagen, Alveolar Cell, Lung Diseases, So, Type-II Pneumocyte, Transitional Epithelial Cell, dTAF[[II]]230, Noise, preventive therapy, pulmo, cyclopism, statistics and numerical data, Expression Profiles, mouse, MYH-associated polyposis, lung parenchyma, TAF200, Monitorings, Pollution, autosomal recessive familial adenomatous polyposis, Adenomatous, Maps, Squamous, TAFII-250, TAF250/230, Meyer-Schwickerath's syndrome, Transitional Epithelial, Spectrum Analysis, Cryptophthalmos-Syndactyly Syndrome, Spectroscopy, Gene Expression, Type-I, TAFII250, Fraser, Expression Signatures, Mini-ICE, Diseases, numerical data, Expression Profile, neoplasms, Alveolar Epithelial Cell, autosomal recessive, Transcriptome Profiles, Adenomatous Epithelial Cell, Mus musculus, RUTBC3, Adenomatous Epithelial Cells, Squamous Cell, Caspase-14 subunit p10, Epigenetic, Death Cause, Transcriptome Profilings, mice, Swiss Mouse, Spectrometry, Caspase-14 subunit p19, Type 2, CG17603, MICE, TAF[[II]], cell_type, Pulmonary Diseases, respiratory conducting tube, domesticus, Type 1, RABGAP5, Cryptophthalmos Syndactyly Syndrome, Alveolar Epithelial, DMDA, airway, Gene Expression Analyses, pulmonary, Taf250, disease or disorder of lung, SR3-5, Cells, multiple colorectal, Death Causes, Collagen Felt, Expression Analysis, Mouse, Noise Pollution, Type 1 Pneumocyte, pulmonary diseases, Epigenetics, Proteomes, Cryptophthalmos-Syndactyly Syndromes, TAF230, Type II Pneumocytes, 3.4.22.-, d230, Lung Disease, Lung, Type 2 Pneumocyte, lung disorders, Peptidomics, Transcriptome Profile, Ulrich-Feichtiger syndrome, Matrix, alpha-Collagen, Gene, dTAFII250, mini-ICE, Glandular Epithelial, Spectrum Analyses, Matrices, EfW1, TYPE, Gene Expression Profilings, DAGA4, mRNA Differential Displays, Gene Expression Pattern Analysis, Squamous Epithelial Cells, Microfibril, Pulmonary Disease, utilization, dmTAF1, DmelCG11121, House, Taf230, Dermodress, Collastat, lung, Mass, Gene Products, Mus musculus domesticus, MAM, neoplasm, Mice, SCG3, Squamous Epithelial, familial adenomatous polyposis, Mass Spectroscopy, MAP, Pulmonary, Type I Pneumocytes, TAF250, Epithelial, Taf200, disease of lung, cholesterol synthesis, matrisome, somda, dTAF[[II]]250, airways, cell, Swiss, Profile, familial adenomatous polyposis 2, cholesterol formation, Avitene, Type 2 Pneumocytes, segment of tracheobronchial tree, Taf1p, Transcriptomics, PULM DIS, Transcript Expression, Transcriptome Analysis, alpha Collagen, Monitoring, Type 1 Pneumocytes, autosomal recessive multiple colorectal adenomas, parenchyma of lung., Pneumocyte, dTAF250, pulmonary disease, Epithelial Cells, Transitional Epithelial Cells, Extracellular, Syndrome, Pneumocytes, Chronic, TAF, Expression Analyses, Squamous Epithelial Cell, Collagenfleece, Glandular Epithelial Cell, Controlled, Drl, Transitional, Profiling, Squamous Cells, Disease, Controlling, TAF[[II]]250, use, Transcriptome, MUTYH-Associated Polyposis, Fraser-Francois syndrome, Type-I Pneumocyte, lung disease or disorder, Proteins, total expressed protein, l(3)84Ab, function, BG:DS00004.13, Cell, Mdu, LGMD2C, dTAF230, Differential Display, Alveolar Cells, Transcript Expression Analyses, MS, Cuboidal Glandular Epithelial Cells, native protein, tracheobronchial tree segment, Mus, mda, p230, Protein, Gene Expression Signatures, Collagen Hemostat, TAF[[II]]250/230, TFIID, cholesterol biosynthesis, Gene Expression Signature, Columnar Glandular Epithelial Cells, DIS PULM, mRNA Differential Display, Mass Spectrum Analyses, ami, Pangen, Taf[[II]]250, Mass Spectrum, Gene Expression Monitoring, TAF[[II]]230, Transcriptome Profiling, DMDA1, mRNA, med, prophylaxis, other collagen, cryptophthalmos with Other malformations, Glandular Epithelial Cells, House Mice, Avicon, TAF[II]250, Type-I Pneumocytes, Differential Displays, MYH-Associated Polyposis, Transcriptome Analyses, cryptophthalmos syndrome, Noises, Laboratory Mice, Protein Gene Products, Gene Proteins, DmelCG17603, control, Gene Expression Profiles, SCARMD2, Cryptophthalmos with Other Malformations, MAP syndrome, Lungs, Signature, General activity, Laboratory Mouse, proteinaceous extracellular matrix, FAP2, TAF1, colorectal adenomatous polyposis0falseM.musculus - Lung, iBAQ (Angelidisetal,natcommun.2019)abundance based on iBAQ, Interaction consistency score: 9.7, Coverage: 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