{"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"},"statusCode":"OK","statusCodeValue":200}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Christian von Mering"],"species":["10116"],"full_dataset_link":["https://pax-db.org/dataset/10116/3360659913"],"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":["Highly aggressively proliferating immortalized (HAPI) microglial cells have been used as an in vitro model for investigating key microglial functions including inflammatory, neurotoxic, and phagocytic activities. Through the use of offline strong cation-exchange fractionation followed by inline reversed-phase chromatographic separation and tandem mass spectrometric analysis on a hybrid linear ion trap-Orbitrap instrument, the HAPI microglial proteome was characterized to a depth of 3006 unique protein groups. Upon bioinformatic analysis of the HAPI proteome data set, enrichment was observed for processes relevant to microglial function including those associated with immune system response. This study marks the most comprehensive reference data set generated to date for the rat microglial proteome."],"pubmed_title":["Proteomic analysis of rat microglia establishes a high-confidence reference data set of over 3000 proteins."],"pubmed_authors":["Bell-Temin Harris H, Barber David S DS, Zhang Ping P, Liu Bin B, Stevens Stanley M SM"],"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"],"pubmed_title_synonyms":["brown rat, MF.microglia.CNS, microglial cell, Rat, Rattus norvegicus, norvegicus, Data Set, Hortega cell, Laboratory, Protein., Microglial Cell, brain-resident macrophage, Proteins, Norway Rat, Gene, proteins, Rattus, rats, Norway Rats, microgliocyte, microglia, Cell, Laboratory Rat, Microglial, Protein Gene Products, Gene Proteins, rat, Rattus sp. strain Wistar, Mus norvegicus, Rats, Rattus norwegicus, native protein, Mammals, Laboratory Rats, Protein, proteomic analysis, Gene Products, Norway rat, brain macrophage, hortega cells, Norway, Rattus rattiscus, Microglias, Microglial Cells, Rattus norvegicus8, Gunn rats"],"name_synonyms":["Microglial, Peptidomics., MF.microglia.CNS, microglial cell, Hortega cell, Microglial Cell, brain-resident macrophage, brain macrophage, hortega cells, Microglias, microgliocyte, Microglial Cells, microglia, Cell"],"pubmed_abstract_synonyms":["Kation, Hybrids, Rat, Immune Systems, norvegicus, determination, Laboratory, cation, instrument configuration, FBN, Gene, Norway Rat, protein, protein-containing complex, Norway Rats, dIKK-gamma, hardware, Microglial, protrusion, protein polypeptide chains, rat, Rattus sp. strain Wistar, Rats, resilient, polypeptide chain, ECTOL1, Mammals, DmIKK-gamma, tough, responsivity, Gene Products, Norway rat, dmIKKgamma, Rattus rattiscus, IKK[[gamma]], protein aggregate, Microglias, Separated, IKKg, WMS, KEY, Key, brown rat, strong, reactivity, study, Divorced, Rattus norvegicus, Microglial Cell, HardwareType, Divorces, proteins, Chimeras, Laboratory Rat, OCTD, cations, Immune, IKK, Cation, GPHYSD2, SGS, Rattus norvegicus8, anatomical protrusion, Data Set, protein complex, Proteins, Kationen, total expressed protein, function, Rattus, backward, Cell, cationes, ACMICD, IKKgamma, DmIKKgamma, Mus norvegicus, Hybrid, native protein, Rattus norwegicus, natural protein, dIKK, Laboratory Rats, chemical analysis, Protein, Systems, Proteomes., Kenny, MFS1, WMS2, Separation, instrument, Dmikkgamma, System, Separations, IKK-gamma, MASS, CG16910, rats, Protein Gene Products, Gene Proteins, DmelCG16910, spine, SSKS, assay, Norway, response, Proteomes, Microglial Cells, reversed, Gunn rats"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"R.norvegicus - Microglial cell, SC (Bell-temin,proteomics,2012)","description":"abundance based on Spectral counting, Interaction consistency score: 20.2, Coverage: 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