PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimary200OK0000ProteomicsChristian von Mering10116https://pax-db.org/dataset/10116/3089243329mering@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 is associated with the decline of protein, cell, and organ function. Here, we use an integrated approach to characterize gene expression, bulk translation, and cell biology in the brains and livers of young and old rats. We identify 468 differences in protein abundance between young and old animals. The majority are a consequence of altered translation output, that is, the combined effect of changes in transcript abundance and translation efficiency. In addition, we identify 130 proteins whose overall abundance remains unchanged but whose sub-cellular localization, phosphorylation state, or splice-form varies. While some protein-level differences appear to be a generic property of the rats' chronological age, the majority are specific to one organ. These may be a consequence of the organ's physiology or the chronological age of the cells within the tissue. Taken together, our study provides an initial view of the proteome at the molecular, sub-cellular, and organ level in young and old rats.Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats.Ori Alessandro A, Toyama Brandon H BH, Harris Michael S MS, Bock Thomas T, Iskar Murat M, Bork Peer P, Ingolia Nicholas T NT, Hetzer Martin W MW, Beck Martin MAdd, 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, ratioRat, Transcriptome, norvegicus, Transcriptome Profile, Laboratory, Expression Profiles, Gene Expression Profile, total expressed protein, Gene, Norway Rat, Profiles, Rattus, Norway Rats, element, Mdu, CG11121, whole transcriptome, Gene Expression, rat, Rattus sp. strain Wistar, Mus norvegicus, old, Rattus norwegicus, Rats, DmelCG11121, mda, Expression Signatures, Laboratory Rats, Gene Expression Signatures, Norway rat, Gene Expression Signature, Rattus rattiscus, Expression Profile, ami, Transcriptome Profiles, organ, brown rat, somda, Rattus norvegicus, med, Profile, rats, Signatures, SO, Laboratory Rat., Expression Signature, Gene Expression Profiles, anatomical unit, body organ, Transcriptomes, Norway, Signature, Proteomes, So, Drl, Rattus norvegicus8, Gunn ratsjecur, iecur., Liversprotein translation, AT1G11140, Forms, Rat, d230, norvegicus, establishment and maintenance of localization in cell or cell membrane, Laboratory, metazoans, Gene, Norway Rat, dTAFII250, protein, Aging, Cell Biologies, protein-containing complex, EfW1, animals, Norway Rats, phosphorylation, element, CG11121, CG12298, Productivity, SUB, dmTAF[[II]]230, protein polypeptide chains, rat, Rattus sp. strain Wistar, intracellular localization, old, Rats, polypeptide chain, dmTAF1, DmelCG11121, DmelCG12298, Biological, Taf230, Gene Products, SCRAMBLED, Norway rat, Rattus rattiscus, Animal, protein aggregate, KIF20A, TAF250, organ, brown rat, Animalia, Senescence, portion of tissue, study, single organism cellular localization, Taf200, somda, dTAF[[II]]250, Rattus norvegicus, Gene Expressions, TFIID TAF250, Biology, single-organism cellular localization, cel, cell, mei-1794, Tissue, localization within cell, Taf1p, proteins, Cellular Biologies, Dietary Fiber, Expressions, SO, Laboratory Rat, Laboratory Rat., dTAF250, Biological Aging, anatomical unit, body organ, SRF9, Expression, TAF, So, Drl, Rattus norvegicus8, protein anabolism, dTAF[[II]]230, TAF[[II]]250, protein biosynthetic process, protein complex, Cellular Biology, Proteins, Biologies, STRUBBELIG, TAF200, Phosphorylations, total expressed protein, l(3)84Ab, BG:DS00004.13, function, Rattus, TAFII-250, TAF250/230, INSDC_feature:misc_RNA, Cell, Mdu, dTAF230, STRUBBELIG-RECEPTOR FAMILY 9, TAFII250, Mus norvegicus, native protein, Rattus norwegicus, natural protein, mda, p230, Laboratory Rats, Protein, Metazoa, protein formation, TAF[[II]]250/230, tissue portion, TFIID, protein biosynthesis, Cellular, phosphorylation enrichment, simple tissue, ami, cellular localisation, Taf[[II]]250, TAF[[II]]230, med, Dub, TAF[II]250, establishment and maintenance of cellular localization, CG17603, TAF[[II]], rats, Protein Gene Products, multicellular animals, Gene Proteins, Livers, DmelCG17603, Taf250, protein synthesis, SR3-5, Norway, T19D16.8, Proteomes, SCM, TAF230, TAF1, Gunn rats0falseR.norvegicus - Liver, SC (Orietal,cellsyst2015)abundance based on Spectral counting, Interaction consistency score: 14.6, Coverage: 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