PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimary200OK0000ProteomicsChristian von Mering6239https://pax-db.org/dataset/6239/1475773660mering@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 nematode Caenorhabditis elegans is a popular model system in genetics, not least because a majority of human disease genes are conserved in C. elegans. To generate a comprehensive inventory of its expressed proteome, we performed extensive shotgun proteomics and identified more than half of all predicted C. elegans proteins. This allowed us to confirm and extend genome annotations, characterize the role of operons in C. elegans, and semiquantitatively infer abundance levels for thousands of proteins. Furthermore, for the first time to our knowledge, we were able to compare two animal proteomes (C. elegans and Drosophila melanogaster). We found that the abundances of orthologous proteins in metazoans correlate remarkably well, better than protein abundance versus transcript abundance within each organism or transcript abundances across organisms; this suggests that changes in transcript abundance may have been partially offset during evolution by opposing changes in protein abundance.Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes.Schrimpf Sabine P SP, Weiss Manuel M, Reiter Lukas L, Ahrens Christian H CH, Jovanovic Marko M, Malmström Johan J, Brunner Erich E, Mohanty Sonali S, Lercher Martin J MJ, Hunziker Peter E PE, Aebersold Ruedi R, von Mering Christian C, Hengartner Michael O MOAdd, 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, rationematode, fruit fly, Drosophila, determination, elegan, Drosophila melangaster, Drosophila melanogasters, chemical analysis, Proteomes., assay, Sophophora melanogaster, Caenorhabditis, Rhabditis elegans, melanogaster, Caenorhabditis elegan, D. melanogasterKoerper., organism, whole body, multi-cellular organism, whole organism, animal, bodyother disease, fruit fly, Materials, multi-cellular organism, Peptidomics, Effects, elegan, metazoans, Gene, Sophophora melanogaster, protein, melanogaster, protein-containing complex, animals, body system, Long Term, protein polypeptide chains, Tier, diseases, polypeptide chain, Roles, heredity, Drosophila melangaster, Gene Products, disease or disorder, Concepts, system, diseases and disorders, Animal, protein aggregate, animal, Effect, Animalia, human disease, anatomical systems, Genetic, Genomes, Longterm, proteins, metazoa, Long-Term, Caenorhabditis elegan, non-neoplastic, roundworm, nematode, nematodes, Role Concepts, roundworms, disorder, Homo sapiens disease, Long-Term Effect, species, Long-Term Effects, Gene., Nemata, body, protein complex, animalia, Proteins, disorders, Longterm Effect, total expressed protein, whole body, medical condition, Cistrons, D. melanogaster, INSDC_feature:misc_RNA, predicted, Concept, organism, Role Concept, native protein, Operons, natural protein, Protein, Long Term Effects, Metazoa, Role, condition, Genetic Materials, connected anatomical system, Rhabditis elegans, Genetic Material, Epistemology, whole organism, whole genome, Caenorhabditis, Longterm Effects, organ system, Protein Gene Products, multicellular animals, Gene Proteins, disease, Drosophila, Material, Drosophila melanogasters, Koerper, Cistron, Proteomes0falseC.elegans - Whole organism, Dauer, SC (Schrimpf,plos_biology,2009)abundance based on Spectral counting, Dauer, Interaction consistency score: 12.8, Coverage: 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