{"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":["99287"],"full_dataset_link":["https://pax-db.org/dataset/99287/2856723965"],"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":["Salmonella enterica serovar Typhimurium (also known as Salmonella typhimurium) is a facultative intracellular pathogen that causes approximately 8,000 reported cases of acute gastroenteritis and diarrhea each year in the United States. Although many successful physiological, biochemical, and genetic approaches have been taken to determine the key virulence determinants encoded by this organism, the sheer number of uncharacterized reading frames observed within the S. enterica genome suggests that many more virulence factors remain to be discovered. We used a liquid chromatography-mass spectrometry-based \"bottom-up\" proteomic approach to generate a more complete picture of the gene products that S. typhimurium synthesizes under typical laboratory conditions as well as in culture media that are known to induce expression of virulence genes. When grown to logarithmic phase in rich medium, S. typhimurium is known to express many genes that are required for invasion of epithelial cells. Conversely stationary phase cultures of S. typhimurium express genes that are needed for both systemic infection and growth within infected macrophages. Lastly bacteria grown in an acidic, magnesium-depleted minimal medium (MgM) designed to mimic the phagocytic vacuole have been shown to up-regulate virulence gene expression. Initial comparisons of protein abundances from bacteria grown under each of these conditions indicated that the majority of proteins do not change significantly. However, we observed subsets of proteins whose expression was largely restricted to one of the three culture conditions. For example, cells grown in MgM had a higher abundance of Mg(2+) transport proteins than found in other growth conditions. A second more virulent S. typhimurium strain (14028) was also cultured under these same growth conditions, and the results were directly compared with those obtained for strain LT2. This comparison offered a unique opportunity to contrast protein populations in these closely related bacteria. Among a number of proteins displaying a higher abundance in strain 14028 were the products of the pdu operon, which encodes enzymes required for propanediol utilization. These pdu operon proteins were validated in culture and during macrophage infection. Our work provides further support for earlier observations that suggest pdu gene expression contributes to S. typhimurium pathogenesis."],"pubmed_title":["Analysis of the Salmonella typhimurium proteome through environmental response toward infectious conditions."],"pubmed_authors":["Adkins Joshua N JN, Mottaz Heather M HM, Norbeck Angela D AD, Gustin Jean K JK, Rue Joanne J, Clauss Therese R W TR, Purvine Samuel O SO, Rodland Karin D KD, Heffron Fred F, Smith Richard D RD"],"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":["reactivity, Salmonella choleraesuis serotype typhimurium, Salmonella typhi-murium, Salmonella enterica ser. typhimurium, Salmonella enterica serovar Typhimurium, determination, Salmonella typhimurium, Samonella typhimurium, total expressed protein, 12, [5], Salmonella enterica subsp. enterica serovar 1, responsivity, chemical analysis, 2, 4, assay, Salmonella enterica serotype Typhimurium, response, Salmonella typhimurium LT2, clinical infection., Bacillus typhimurium, Proteomes, :i:1, 12:i:1, Salmonella enterica 1"],"name_synonyms":["l(3)Ca, multi-cellular organism, body, mCRY, titin, whole body, 26S protease, l(3)62Ca, d-titin, 0020/01, threonine endopeptidase activity, Mbh1, SLS, Sls, ingensin, kettin, organism, large multicatalytic protease, CFU-MC, HEL-S-66, DmelCG1915, Titin, prosome, Crry, multicatalytic endopeptidase complex, animal, anon-CREST, Ket, CFU-Mast, tricorn proteinase, D-titin, l(3)j1D7, whole organism, AFCP, colony forming unit mast cell, D-Titin, CG18857, MIC10, ket, sam, sal, TLX, l(3)dre8, lens neutral proteinase, CG1915, CT41299, multicatalytic proteinase (complex), Koerper, proteasome endopeptidase complex., KZ, polyhedral organelle, l(3)S002001, l(3)rL182, CG18242, tricorn protease, AHUS2, TRA2.10, Mcp, MCP, alkaline protease, multicatalytic proteinase, CG18245"],"pubmed_abstract_synonyms":["Virulence, nucleocytoplasm, Materials, Epithelial Cell, The runs, Laboratory, Vacuole, postnatal development, Liquid Chromatography Mass Spectrometry, positive regulation by symbiont of host non-apoptotic programmed cell death, High Performance Liquid Chromatography Mass Spectrometry, Infestations and Infections, growth and development, Ultra Performance Liquid Chromatography-Mass Spectrometry, protein, Glandular, infectivity, Reading Frame, anterior midline glia, High Performance Liquid Chromatography-Mass Spectrometry, 12, solute:solute exchange, protein polypeptide chains, Background, HPLC-MS, Liquid Chromatography-Mass, macrophage, Cultural, CG9063, Monocyte-Derived Macrophage, pathogenesis, 2, 4, median glial cell, protein aggregate, animal, IKKg, KEY, Key, viral infection, Ultra Performance Liquid Chromatography Mass Spectrometry, ethnicity, modification by symbiont of host biological process, Eubacteria, Gene Expressions, Salmonella enterica serovar Typhimurium, enzymes, stimulation by symbiont of host programmed cell death, Genomes, Diarrheas, magnesio, U.S., Adenomatous Epithelial, proteins, BcDNA:GH03694, ecotype, genetic, Bacteria Woese et al. 2024, Pathogenicity Factors, [5], Bacteria <bacteria>, Liquid Chromatography-Mass Spectrometries, Prokaryotae, s, Procaryotae, Strains, Infections and Infestations, intracellular, DmelCG9063, Transitional Epithelial Cell, close to, typical plasmatocyte, Gastroenteritides, familial, Adenomatous, The trots, Squamous, monocyte-derived macrophage, Transitional Epithelial, results, Acute onset, Virulence Factor, DmIKKgamma, organism, Cultural Background, Cultures, Operons, single-organism transport, dIKK, diarrhea of presumed infectious origin, Kenny, Pathogenicity, modulation by symbiont of host system process, Genetic Materials, prokaryotes, midline glia, cultivar, laboratory, internal to cell, Diarrhoea, Genetic Material, Monocyte-Derived Macrophages, Adenomatous Epithelial Cell, Adenomatous Epithelial Cells, Squamous Cell, Factors, whole organism, Cultural Beliefs, growth pattern, High Pressure Liquid Chromatography Mass Spectrometry, non-developmental growth, BcDNAGH03694, IKK-gamma, Spectrometry, Infection and Infestation, INSDC_feature:gene, whole genome, induction by organism of programmed cell death in other organism during symbiotic interaction, 3L6, DmelCG16910, rich, Material, activation by symbiont of host programmed cell death, Koerper, Cells, Biocatalyst, Liquid, small molecule transport, Cistron, inherited genetic, histiocyte, Strains and Sprains, :i:1, Prokaryota, 12:i:1, Salmonella typhi-murium, multi-cellular organism, vacuolar carboxypeptidase Y, Monocyte Derived Macrophages, Biocatalysts, regulation by symbiont of host system process, number, Gene, Glandular Epithelial, eubacteria, protein-containing complex, dIKK-gamma, Frames, Squamous Epithelial Cells, magnesium, polypeptide chain, induction by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction, DmIKK-gamma, Pathogenicity Factor, Gene Products, dmIKKgamma, Bacteriobiota, IKK[[gamma]], Sprains, agranular plasmatocyte, Bacillus typhimurium, Squamous Epithelial, Backgrounds, Epithelial, protoplasm, Frame, UPLC-MS, induction of non-apoptotic programmed cell death by other organism, Ultra-Performance Liquid Chromatography-Mass Spectrometry, Genetic, protoplast, Spectrometries, Cultural Relativisms, Bone Marrow-Derived Macrophage, causes, Expressions, clinical infection, Monera, modification by symbiont of host morphology or physiology., Bone Marrow-Derived, Bacteria (ex Cavalier-Smith 1987), Infestation and Infection, Enzyme, IKK, lamellocyte, Epithelial Cells, Transitional Epithelial Cells, causality, Customs, species, fungi, Expression, culture, Chromatography-Mass Spectrometries, infectious colitis, constitutitional genetic, Squamous Epithelial Cell, Glandular Epithelial Cell, Transitional, macrophagocyte, Squamous Cells, Salmonella choleraesuis serotype typhimurium, bacteria, disruption by symbiont of host cell, activation by organism of non-apoptotic programmed cell death in other organism, hemolysin activity, body, 12Mg, protein complex, Salmonella typhimurium, Samonella typhimurium, Proteins, Sprain, cell cycle quiescence, whole body, enzyme activity, Factor, High Pressure Liquid Chromatography-Mass Spectrometry, Monocyte Derived, Cultural Backgrounds, diarrhoea of presumed infectious origin, MG, Cistrons, Magnesium, AMG, Cell, Culture, strain, near to, development, IKKgamma, Monocyte-Derived, Diarrhea, Media, Cuboidal Glandular Epithelial Cells, native protein, natural protein, Protein, Strain, Infection, Salmonella enterica serotype Typhimurium, Columnar Glandular Epithelial Cells, Mg, Salmonella enterica 1, Macrophage, Watery stool, United States of America, Salmonella enterica ser. typhimurium, Dmikkgamma, Macrophages, not Bacteria Haeckel 1894, postnatal growth, Glandular Epithelial Cells, Bone Marrow Derived Macrophages, CG16910, Protein Gene Products, ventral midline glia, Gene Proteins, Salmonella enterica subsp. enterica serovar 1, stationary phase, MGA, approaches, prokaryote, vicinity of, cardinality, Chromatography-Mass Spectrometry, Bone Marrow-Derived Macrophages, granulocyte, Reading, LC-MS, MGM, Relativisms, virulence, enteritis and gastroenteritis, Salmonella typhimurium LT2, Relativism, Cultural Relativism, hereditary, growth"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"S.enterica - Whole organism, SC (Adkins,mcp,2006)","description":"abundance based on Spectral counting, Interaction consistency score: 11.4, Coverage: 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