{"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"},"statusCodeValue":200,"statusCode":"OK"}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Christian von Mering"],"species":["9606"],"full_dataset_link":["https://pax-db.org/dataset/9606/4221675112"],"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":["Dengue is an important and growing public health problem worldwide with an estimated 100million new clinical cases annually. Currently, no licensed drug or vaccine is available. During natural infection in humans, liver cells constitute one of the main targets of dengue virus (DENV) replication. However, a clear understanding of dengue pathogenesis remains elusive. In order to gain a better reading of the cross talk between virus and host cell proteins, we used a proteomics approach to analyze the host response to DENV infection in a hepatic cell line Huh-7. Differences in proteome expression were assayed 24h post-infection using label-free LC-MS. Quantitative analysis revealed 155 differentially expressed proteins, 64 of which were up-regulated and 91 down-regulated. These results reveal an important decrease in the expression of enzymes involved in the glycolytic pathway, citrate cycle, and pyruvate metabolism. This study provides large-scale quantitative information regarding protein expression in the early stages of infection that should be useful for better compression of the pathogenesis of dengue.<h4>Biological significance</h4>Dengue infection involves alterations in the homeostasis of the host cell. Defining the interactions between virus and cell proteins should provide a better understanding of how viruses propagate and cause disease. Here, we present for the first time the proteomic analysis of hepatocytes (Huh-7 cells) infected with DENV-2 by label-free LC-MS."],"pubmed_title":["Quantitative proteomic analysis of Huh-7 cells infected with Dengue virus by label-free LC-MS."],"pubmed_authors":["Pando-Robles Victoria V, Oses-Prieto Juan A JA, Rodríguez-Gandarilla Myriam M, Meneses-Romero Erika E, Burlingame Alma L AL, Batista Cesar V F CV"],"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"],"description_synonyms":["Huh-7, Huh7."],"pubmed_title_synonyms":["UPLC-MS, Ultra Performance Liquid Chromatography Mass Spectrometry, Ultra-Performance Liquid Chromatography-Mass Spectrometry, HuH-7, Viruses, High Pressure Liquid Chromatography Mass Spectrometry, Breakbone Fever Viruses, Liquid Chromatography Mass Spectrometry, number, Fever Virus, Spectrometry, High Performance Liquid Chromatography Mass Spectrometry, Breakbone Fever, Spectrometries, Ultra Performance Liquid Chromatography-Mass Spectrometry, High Pressure Liquid Chromatography-Mass Spectrometry, RCB1942, presence, free, Cell, Huh7, RCB1366, Fever Viruses, count in organism, Dengue, HPLC-MS, Huh-7, Liquid Chromatography-Mass, label, Liquid Chromatography-Mass Spectrometries, Chromatography-Mass Spectrometry, proteomic analysis, Virus, Liquid, LC-MS, Chromatography-Mass Spectrometries, Dengue Viruses, High Performance Liquid Chromatography-Mass Spectrometry., Breakbone, Breakbone Fever Virus"],"name_synonyms":["Line, Peptidomics., Cell Lines, Huh-7, Cell, Huh7, Lines"],"pubmed_abstract_synonyms":["Viridae, Classical Dengues, host organism, scale tissue, Product, determination, fond, Liquid Chromatography Mass Spectrometry, positive regulation by symbiont of host non-apoptotic programmed cell death, Mbp1, Infestations and Infections, High Performance Liquid Chromatography Mass Spectrometry, Hepatocyte, ion(3-), Break-Bone Fever, Ultra Performance Liquid Chromatography-Mass Spectrometry, protein, sci, CycEI, Long Term, High Performance Liquid Chromatography-Mass Spectrometry, dmTAF[[II]]230, Readability, protein polypeptide chains, HPLC-MS, Liquid Chromatography-Mass, Ccne, diseases, Hepatic Cell, Break Bone Fever, Pharmaceutical Product, Virus, Line, pathogenesis, HOW, How, 2, diseases and disorders, hemorrhagic dengue, protein aggregate, myd, Fs(3)Hor, Effect, l(3)j5D5, 24B, Ultra Performance Liquid Chromatography Mass Spectrometry, modification by symbiont of host biological process, DmelCG2684, human disease, Man (Taxonomy), stimulation by symbiont of host programmed cell death, enzymes, TFIID TAF250, cel, plant peltate hair, stru, iecur, Mbp-1, proteins, l(3)S053606, NTef2, inhibition of homeostatic process, Estimated, CG10293, Community Health, free, Fever Viruses, l(3)j5B5, citrate, medicine, Vira, Pharmaceutical, Liquid Chromatography-Mass Spectrometries, Fever, homeostasis, Homo sapiens disease, Infections and Infestations, Breakbone, Long-Term Effects, 0904/17, dTAF[[II]]230, Citrate, PLATEST, gyltl1b-b, Modern, Citric Acid Monohydrate, TAF200, Longterm Effect, 2-hydroxytricarballylate, TAFII-250, Cyc E, br37, TAF250/230, results, Citric Acid, Huh7, Fs(3)Sz11, CITRATE ANION, Hepatic Cells, TAFII250, Dengue fever, BG:DS07108.3, positive regulation of homeostatic process, SZ1, MDDGA6, mKIAA0609, Diseases, modulation by symbiont of host system process, Pharmaceutic, l(2)05206, KIAA0609, High Performance Liquid Chromatography-Mass Spectrometry., Philippine hemorrhagic fever, Break-Bone, Lines, fg, gyltl1b, Thai hemorrhagic fever, High Pressure Liquid Chromatography Mass Spectrometry, Breakbone Fever Viruses, Anhydrous Citric Acid, cit, mdc1d, Fever Virus, Spectrometry, expanded, Breakbone Fever, Infection and Infestation, CG17603, TAF[[II]], induction by organism of programmed cell death in other organism during symbiotic interaction, modification by symbiont of host morphology or physiology, early, 2-hydroxy-1, MDC1D, disease, Health, l35Dd, hyaline, 3-propanetricarboxylate(3-), enr, enlarged, Taf250, label, Horka, SR3-5, activation by symbiont of host programmed cell death, Cells, Biocatalyst, CG2684, Liquid, Fs(3)Horka, Preventive Medicine & Public Health, Animal Viruses, anon-EST:Liang-2.39, Preventive Medicine and Public Health, Dengue Viruses, Classical, Proteomes, Platelets, humans, TAF230, Community, big, Classical Dengue Fevers, other disease, d230, cycline, Dengue Fever, Peptidomics, Effects, Biocatalysts, P62, regulation by symbiont of host system process, DmcyclinE, peltate hair, number, Gene, dTAFII250, cycE, protein-containing complex, pyruvate dehydrogenase bypass, EfW1, presence, l(2)br37, cit(3-), froggy, CYCLE, Gyltl1a, Human, jecur, cdi7, large, cyclinE, Homo sapiens, polypeptide chain, induction by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction, dmTAF1, Taf230, Gene Products, Cdi7, CDI7, disease or disorder, DmF2, Animal, Man, TAF250, Drugs, lod, UPLC-MS, study, induction of non-apoptotic programmed 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condition, qkr, RCB1942, l(3)S090417, Cell, dTAF230, viruses, count in organism, l(2)k02514, Classical Dengue, native protein, DmCycE, natural protein, Public, p230, KH93F, Protein, chemical analysis, Long Term Effects, Singapore hemorrhagic fever, proteomic analysis, Infection, classical dengue, TAF[[II]]250/230, TFIID, condition, CyeE, scales, Zoophaginae, Environment, regulation of homeostatic process, Breakbone Fever Virus, who, Taf[[II]]250, Uralyt U, l(2)k02602, TAF[[II]]230, scale, Pharmaceutic Preparations, l(2)35Dd, TAF[II]250, Who/How, Understanding, Lds, 3-propanetricarboxylic acid, Longterm Effects, RCB1366, Drug, Protein Gene Products, Livers, Gene Proteins, D-CycE, Preparations, Dengue, activation of homeostatic process, DmelCG17603, clear, Huh-7, Classical Dengue Fever, Vaccine, Modern Man, Chromatography-Mass Spectrometry, qkr[93F], LC-MS, assay, Pharmaceutical Products, CG3938, Pharmaceutical Preparation, 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