System-based proteomic analysis of the interferon response in human liver cells View Full Text


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Article Info

DATE

2004-07-22

AUTHORS

Wei Yan, Hookeun Lee, Eugene C Yi, David Reiss, Paul Shannon, Bartlomiej K Kwieciszewski, Carlos Coito, Xiao-jun Li, Andrew Keller, Jimmy Eng, Timothy Galitski, David R Goodlett, Ruedi Aebersold, Michael G Katze

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. More... »

PAGES

r54

References to SciGraph publications

  • 2000-12. A network of protein–protein interactions in yeast in NATURE BIOTECHNOLOGY
  • 1999-10. Protein tyrosine kinase-mediated pathways in G protein-coupled receptor signaling in CELL BIOCHEMISTRY AND BIOPHYSICS
  • 2003-04. Cdc42 & GSK-3: signals at the crossroads in NATURE CELL BIOLOGY
  • 2002-03. Host cell proteins binding to the encapsidation signal ɛ in hepatitis B virus RNA in ARCHIVES OF VIROLOGY
  • 2002-09. Viruses and interferon: a fight for supremacy in NATURE REVIEWS IMMUNOLOGY
  • 2003-04-01. GoMiner: a resource for biological interpretation of genomic and proteomic data in GENOME BIOLOGY
  • 1998-09-17. Cell growth control by G protein-coupled receptors: from signal transduction to signal integration in ONCOGENE
  • 2003-03. Involvement of YY1 and its correlation with c-myc in NDEA induced hepatocarcinogenesis, its prevention by d-limonene in MOLECULAR BIOLOGY REPORTS
  • 2003-03-27. PreBIND and Textomy – mining the biomedical literature for protein-protein interactions using a support vector machine in BMC BIOINFORMATICS
  • 1998-12-31. EB1, a protein which interacts with the APC tumour suppressor, is associated with the microtubule cytoskeleton throughout the cell cycle in ONCOGENE
  • 1999-10. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags in NATURE BIOTECHNOLOGY
  • 2001-10. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry in NATURE BIOTECHNOLOGY
  • 1994-11-01. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database in JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
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    http://scigraph.springernature.com/pub.10.1186/gb-2004-5-8-r54

    DOI

    http://dx.doi.org/10.1186/gb-2004-5-8-r54

    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/15287976


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