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Quantitative Imaging Analysis of NF-κB for Mathematical Modeling Applications

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Computational Modeling of Signaling Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2634))

Abstract

Mathematical models can integrate different types of experimental datasets, reconstitute biological systems in silico, and identify previously unknown molecular mechanisms. Over the past decade, mathematical models have been developed based on quantitative observations, such as live-cell imaging and biochemical assays. However, it is difficult to directly integrate next-generation sequencing (NGS) data. Although highly dimensional, NGS data mostly only provides a “snapshot” of cellular states. Nevertheless, the development of various methods for NGS analysis has led to much more accurate predictions of transcription factor activity and has revealed various concepts regarding transcriptional regulation. Therefore, fluorescence live-cell imaging of transcription factors can help alleviate the limitations in NGS data by supplementing temporal information, linking NGS to mathematical modeling. This chapter introduces an analytical method for quantifying dynamics of nuclear factor kappaB (NF-κB) which forms aggregates in the nucleus. The method may also be applicable to other transcription factors regulated in a similar fashion.

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Acknowledgments

We thank Mr. Hiroki Michida and Dr. Hiroaki Imoto for discussions on bioinformatics analysis and mathematical modeling, respectively. J.N.W. was supported by the Honjo International Scholarship Foundation. M.O. was supported by JSPS KAKENHI Grant No. 15KT0084, 17H06299, 17H06302, and 18H04031, JST-Mirai program No. JPMJMI19G7, JST-CREST grant JPMJCR21N3, the Takeda Science Foundation, and the Uehara Memorial Foundation.

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Authors and Affiliations

  1. Institute for Protein Research, Osaka University, Suita, Osaka, Japan

    Johannes Nicolaus Wibisana & Mariko Okada

  2. Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Resaerch, Hirosawa, Wako, Japan

    Takehiko Inaba & Yasushi Sako

  3. Center for Drug Design and Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan

    Mariko Okada

Authors
  1. Johannes Nicolaus Wibisana
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  2. Takehiko Inaba
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  3. Yasushi Sako
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  4. Mariko Okada
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Corresponding author

Correspondence to Mariko Okada .

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Editors and Affiliations

  1. Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia

    Lan K. Nguyen

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Wibisana, J.N., Inaba, T., Sako, Y., Okada, M. (2023). Quantitative Imaging Analysis of NF-κB for Mathematical Modeling Applications. In: Nguyen, L.K. (eds) Computational Modeling of Signaling Networks. Methods in Molecular Biology, vol 2634. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3008-2_11

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  • DOI: https://doi.org/10.1007/978-1-0716-3008-2_11

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3007-5

  • Online ISBN: 978-1-0716-3008-2

  • eBook Packages: Springer Protocols

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