• Title/Summary/Keyword: Network biology

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Systems Biology - A Pivotal Research Methodology for Understanding the Mechanisms of Traditional Medicine

  • Lee, Soojin
    • Journal of Pharmacopuncture
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    • v.18 no.3
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    • pp.11-18
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    • 2015

  • Objectives: Systems biology is a novel subject in the field of life science that aims at a systems' level understanding of biological systems. Because of the significant progress in high-throughput technologies and molecular biology, systems biology occupies an important place in research during the post-genome era. Methods: The characteristics of systems biology and its applicability to traditional medicine research have been discussed from three points of view: data and databases, network analysis and inference, and modeling and systems prediction. Results: The existing databases are mostly associated with medicinal herbs and their activities, but new databases reflecting clinical situations and platforms to extract, visualize and analyze data easily need to be constructed. Network pharmacology is a key element of systems biology, so addressing the multi-component, multi-target aspect of pharmacology is important. Studies of network pharmacology highlight the drug target network and network target. Mathematical modeling and simulation are just in their infancy, but mathematical modeling of dynamic biological processes is a central aspect of systems biology. Computational simulations allow structured systems and their functional properties to be understood and the effects of herbal medicines in clinical situations to be predicted. Conclusion: Systems biology based on a holistic approach is a pivotal research methodology for understanding the mechanisms of traditional medicine. If systems biology is to be incorporated into traditional medicine, computational technologies and holistic insights need to be integrated.

  • https://doi.org/10.3831/KPI.2015.18.020 인용 PDF KSCI

Databases and tools for constructing signal transduction networks in cancer

  • Nam, Seungyoon
    • BMB Reports
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    • v.50 no.1
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    • pp.12-19
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    • 2017

  • Traditionally, biologists have devoted their careers to studying individual biological entities of their own interest, partly due to lack of available data regarding that entity. Large, high-throughput data, too complex for conventional processing methods (i.e., "big data"), has accumulated in cancer biology, which is freely available in public data repositories. Such challenges urge biologists to inspect their biological entities of interest using novel approaches, firstly including repository data retrieval. Essentially, these revolutionary changes demand new interpretations of huge datasets at a systems-level, by so called "systems biology". One of the representative applications of systems biology is to generate a biological network from high-throughput big data, providing a global map of molecular events associated with specific phenotype changes. In this review, we introduce the repositories of cancer big data and cutting-edge systems biology tools for network generation, and improved identification of therapeutic targets.

  • https://doi.org/10.5483/BMBRep.2017.50.1.135 인용 PDF KSCI

Identification of a Variant Form of Cellular Inhibitor of Apoptosis Protein (c-IAP2) That Contains a Disrupted Ring Domain

  • Park, Sun-Mi;Kim, Ji-Su;Park, Ji-Hyun;Kang, Seung-Goo;Lee, Tae Ho
    • IMMUNE NETWORK
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    • v.2 no.3
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    • pp.137-141
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    • 2002

  • Among the members of the inhibitor of apoptosis (IAP) protein family, only Livin and survivin have been reported to have variant forms. We have found a variant form of c-IAP2 through the interaction with the X protein of HBV using the yeast two-hybrid system. In contrast to the wild-type c-IAP2, the variant form has two stretches of sequence in the RING domain that are repeated in the C-terminus that would disrupt the RING domain. We demonstrate that the variant form has an inhibitory effect on TNF-mediated $NF-{\kappa}B$ activation unlike the wild-type c-IAP2, which increases TNFmediated $NF-{\kappa}B$ activation. These results suggest that this variant form has different activities from the wild-type and the RING domain may be involved in the regulation of TNF-induced $NF-{\kappa}B$ activation.

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From proteomics toward systems biology: integration of different types of proteomics data into network models

  • Rho, Sang-Chul;You, Sung-Yong;Kim, Yong-Soo;Hwang, Dae-Hee
    • BMB Reports
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    • v.41 no.3
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    • pp.184-193
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    • 2008

  • Living organisms are comprised of various systems at different levels, i.e., organs, tissues, and cells. Each system carries out its diverse functions in response to environmental and genetic perturbations, by utilizing biological networks, in which nodal components, such as, DNA, mRNAs, proteins, and metabolites, closely interact with each other. Systems biology investigates such systems by producing comprehensive global data that represent different levels of biological information, i.e., at the DNA, mRNA, protein, or metabolite levels, and by integrating this data into network models that generate coherent hypotheses for given biological situations. This review presents a systems biology framework, called the 'Integrative Proteomics Data Analysis Pipeline' (IPDAP), which generates mechanistic hypotheses from network models reconstructed by integrating diverse types of proteomic data generated by mass spectrometry-based proteomic analyses. The devised framework includes a serial set of computational and network analysis tools. Here, we demonstrate its functionalities by applying these tools to several conceptual examples.

  • https://doi.org/10.5483/BMBRep.2008.41.3.184 인용 PDF