ArticleGenome biology2004
System-based proteomic analysis of the interferon response in human liver cells.
Article in Genome biology, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 72 citations in OpenAlex.
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- Selected Ion Extraction of Peptides with Heavy Isotopes and Hydrogen Loss Reduces the Type II Error in Plasma Proteomics.ACS omega · 2025Article
- Deciphering of the Human Interferon-Regulated Proteome by Mass Spectrometry-Based Quantitative Analysis Reveals Extent and Dynamics of Protein Induction and Repression.Frontiers in immunology · 2017Article
- Comparative proteomic analyses demonstrate enhanced interferon and STAT-1 activation in reovirus T3D-infected HeLa cells.Frontiers in cellular and infection microbiology · 2015Article
- MiR-138 downregulates miRNA processing in HeLa cells by targeting RMND5A and decreasing Exportin-5 stability.Nucleic acids research · 2014Article
- HeLa cell response proteome alterations induced by mammalian reovirus T3D infection.Virology journal · 2013Article
- Development of biomarkers for screening hepatocellular carcinoma using global data mining and multiple reaction monitoring.PloS one · 2013Article
- Plasmacytoid dendritic cells and C1q differentially regulate inflammatory gene induction by lupus immune complexes.Journal of immunology (Baltimore, Md. : 1950) · 2012Article
- Activity based protein profiling to detect serine hydrolase alterations in virus infected cells.Frontiers in microbiology · 2012Article
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- Pathway Palette: a rich internet application for peptide-, protein- and network-oriented analysis of MS data.Proteomics · 2010Article
- Multiplexed isobaric tagging protocols for quantitative mass spectrometry approaches to auditory research.Methods in molecular biology (Clifton, N.J.) · 2009Article
- INTERFEROME: the database of interferon regulated genes.Nucleic acids research · 2009Article
- beta(2)microglobulin mRNA expression levels are prognostic for lymph node metastasis in colorectal cancer patients.British journal of cancer · 2008Article
- Hepatitis C virus infection--pathobiology and implications for new therapeutic options.Digestive diseases and sciences · 2007Review
- Selective identification of newly synthesized proteins in mammalian cells using bioorthogonal noncanonical amino acid tagging (BONCAT).Proceedings of the National Academy of Sciences of the United States of America · 2006Article
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- Proteome analysis of liver cells expressing a full-length hepatitis C virus (HCV) replicon and biopsy specimens of posttransplantation liver from HCV-infected patients.Journal of virology · 2005Article
- Lost in the world of functional genomics, systems biology, and translational research: is there life after the Milstein award?Cytokine & growth factor reviewsReview
Corrections and comments
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Authors and funding
14 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundInterferons (IFNs) play a critical role in the host antiviral defense and are an essential component of current therapies against hepatitis C virus (HCV), a major cause of liver disease worldwide. To examine liver-specific responses to IFN and begin to elucidate the mechanisms of IFN inhibition of virus replication, we performed a global quantitative proteomic analysis in a human hepatoma cell line (Huh7) in the presence and absence of IFN treatment using the isotope-coded affinity tag (ICAT) method and tandem mass spectrometry (MS/MS).
resultsIn three subcellular fractions from the Huh7 cells treated with IFN (400 IU/ml, 16 h) or mock-treated, we identified more than 1,364 proteins at a threshold that corresponds to less than 5% false-positive error rate. Among these, 54 were induced by IFN and 24 were repressed by more than two-fold, respectively. These IFN-regulated proteins represented multiple cellular functions including antiviral defense, immune response, cell metabolism, signal transduction, cell growth and cellular organization. To analyze this proteomics dataset, we utilized several systems-biology data-mining tools, including Gene Ontology via the GoMiner program and the Cytoscape bioinformatics platform.
conclusionsIntegration of the quantitative proteomics with global protein interaction data using the Cytoscape platform led to the identification of several novel and liver-specific key regulatory components of the IFN response, which may be important in regulating the interplay between HCV, interferon and the host response to virus infection.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.