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Bioinformatics Tools for Bulk Gene Expression Deconvolution in Diabetic Retinopathy

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Diabetic Retinopathy

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2678))

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Abstract

Retinal neovascularization is one of the leading causes of vision loss and a hallmark of proliferative diabetic retinopathy (PDR). The immune system is observed to be involved in the pathogenesis of diabetic retinopathy (DR). The specific immune cell type that contributes to retinal neovascularization can be identified via a bioinformatics analysis of RNA sequencing (RNA-seq) data, known as deconvolution analysis. Previous study has identified the infiltration of macrophages in the retina of rats with hypoxia-induced retinal neovascularization and patients with PDR through a deconvolution algorithm, known as CIBERSORTx. Here, we describe the protocols of using CIBERSORTx to perform the deconvolution analysis and downstream analysis of RNA-seq data.

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Acknowledgments

This work was supported by grants from the National Health and Medical Research Council of Australia (GNT1185600). The Centre for Eye Research Australia receives Operational Infrastructure Support from the Victorian Government.

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Authors and Affiliations

  1. Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia

    Ru Qi Teh, Guei-Sheung Liu & Jiang-Hui Wang

  2. Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia

    Guei-Sheung Liu

  3. Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, VIC, Australia

    Guei-Sheung Liu

Authors
  1. Ru Qi Teh
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  2. Guei-Sheung Liu
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  3. Jiang-Hui Wang
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Corresponding authors

Correspondence to Guei-Sheung Liu or Jiang-Hui Wang .

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Editors and Affiliations

  1. Centre for Eye Research Australia, University of Melbourne, East Melbourne, VIC, Australia

    Guei-Sheung Liu

  2. Centre for Eye Research Australia, University of Melbourne, East Melbourne, VIC, Australia

    Jiang-Hui Wang

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Teh, R.Q., Liu, GS., Wang, JH. (2023). Bioinformatics Tools for Bulk Gene Expression Deconvolution in Diabetic Retinopathy. In: Liu, GS., Wang, JH. (eds) Diabetic Retinopathy. Methods in Molecular Biology, vol 2678. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3255-0_7

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  • DOI: https://doi.org/10.1007/978-1-0716-3255-0_7

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3254-3

  • Online ISBN: 978-1-0716-3255-0

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