PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering9685https://pax-db.org/dataset/9685/1049965078mering@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.The amyloidoses constitute a group of diseases occurring in humans and animals that are characterized by abnormal deposits of aggregated proteins in organs, affecting their structure and function. In the Abyssinian cat breed, a familial form of renal amyloidosis has been described. In this study, multi-omics analyses were applied and integrated to explore some aspects of the unknown pathogenetic processes in cats. Whole-genome sequences of two affected Abyssinians and 195 controls of other breeds (part of the 99 Lives initiative) were screened to prioritize potential disease-associated variants. Proteome and miRNAome from formalin-fixed paraffin-embedded kidney specimens of fully necropsied Abyssinian cats, three affected and three non-amyloidosis-affected were characterized. While the trigger of the disorder remains unclear, overall, (i) 35,960 genomic variants were detected; (ii) 215 and 56 proteins were identified as exclusive or overexpressed in the affected and control kidneys, respectively; (iii) 60 miRNAs were differentially expressed, 20 of which are newly described. With omics data integration, the general conclusions are: (i) the familial amyloid renal form in Abyssinians is not a simple monogenic trait; (ii) amyloid deposition is not triggered by mutated amyloidogenic proteins but is a mix of proteins codified by wild-type genes; (iii) the form is biochemically classifiable as AA amyloidosis.Multi-omic analyses in Abyssinian cats with primary renal amyloid deposits.Genova Francesca F, Nonnis Simona S, Maffioli Elisa E, Tedeschi Gabriella G, Strillacci Maria Giuseppina MG, Carisetti Michela M, Sironi Giuseppe G, Cupaioli Francesca Anna FA, Di Nanni Noemi N, Mezzelani Alessandra A, Mosca Ettore E, Helps Christopher R CR, Leegwater Peter A J PAJ, Dorso Laetitia L, Longeri Maria 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, ratioCATS, amyloidosis, 6720460F02Rik, Amyloid Substance, amyloidoses, RCS1, Felis catus, amyloidosis (disease), Domestic Cat, Domestic, cat, Amyloid Fibril, Substance, Felis silvestris catus, Amyloid, Felis sylvestris catus, AI115087, Cats, Amyloid Fibrils, systemic amyloidosis, Fibrils, domestic cat, Domestic Cats, Felis domestica, Felis domesticus, cats, amyloid, 2610008F03Rik, Cat, amyloid disease., FibrilKidneys, reniculate kidney.Panomics, Forms, Formol, Materials, RCS1, metazoans, Domestic Cat, A4, Cs-1, prevention, systemic amyloidosis, diseases, domestic cat, Domestic Cats, Methanal, Parafilm, diseases and disorders, 3, 2210418N07, prevention and control, bacterial catalase-peroxidase activity, MIX, Animalia, amyloidosis, human disease, Man (Taxonomy), reference sample, Genomes, CT21282, Formaldehyd, Oxomethane, proteins, Domestic, Substance, Amyloid, genetic, preventive measures, set, haem catalase activity, Homo sapiens disease, CG7776, associated, SIMPLE, Amyloidoses, reniculate kidney, catalase-peroxidase activity, AI315345, equilase activity, preventive therapy, anatomical protrusion, aberrant, Modern, familial, e(Pc), 2.3.1.7, L[[3]]CP3, AI195249, A330009E03Rik, Amyloid Fibrils, catalase reaction, Felis domestica, PIG7, Diseases, Genetic Materials, Amyloid Protein, fixed, GAT, Genetic Material, ACGNAT, MILD1, Multi Omics, Amyloid Substance, amyloidoses, DmelCG7776, hydrogen-peroxide:hydrogen-peroxide oxidoreductase activity, Integrative, whole genome, Felis silvestris catus, Felis sylvestris catus, disease, Kidneys, DMDA, spine, Material, E(PC), DmelLcp3, anon-48Ac, BG:DS02740.11, Cistron, inherited genetic, DROCATHPO, bs36h11.y1, U00145, Proteomes, humans, Gruppe, other disease, atypia, Cas1, GH05739, Carnitine acetylase, conformation, Amyloidogenic, Gene, Amyloid Fibril, animals, TYPE, AI115087, Human, protrusion, Multi-Omics, DAGA4, CrAT, manganese catalase activity, III, Homo sapiens, GH14582, Amyloid A amyloidosis, animal breed, Gene Products, disease or disorder, amyloid, atypical, Animal, caperase activity, MAM, SCG3, Man, DmelCG2043, study, CATS, 6720460F02Rik, lcp3, Genetic, amyloidosis (disease), LCP-3, CatA, CATA, Omics, non-neoplastic, Cats, DmelCG6871, Amyloid Proteins, CP3, Formalin, Catl, grupos, disorder, cats, Pan-Omics, constitutitional genetic, relational structural quality, Controlled, TP53I7, Controlling, data, DMCATHPO, Integrative-Omics, LcpIII, grupo, heme catalase activity, Felis catus, Proteins, disorders, total expressed protein, medical condition, defective, function, Integrative Omics, Cistrons, Carnitine acetyltransferase, group, LGMD2C, Amyloidogenic Protein, native protein, Felis domesticus, Metazoa, Protein, Multi-Omic, Pan Omics, condition, FORMALIN, MIXL, Cat, CAT, LCP3, amyloid disease, Fibril, optidase activity, CS1, Cas-1, DMLCP3, DMDA1, ensemble, l(2)28-28-12, prophylaxis, Rest, anon-35Fa, amyloidosis AA, CG6871, cat, amyloid A amyloidosis., Methylene oxide, Protein Gene Products, multicellular animals, DmelCG5861, Gene Proteins, Fibrils, Oxomethylene, Cat01, control, anon-35Fc, Modern Man, SCARMD2, 2610008F03Rik, CG2043, hereditary, groupe0falseFcatus - Kidney, iBAQ (Genovaetal,scirep2021)abundance based on iBAQ, Interaction consistency score: 6.0, Coverage: 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