Pathway based-analysis of transcriptomic data from vitamin D studies

Chris T.A. Evelo; Susan L.M. Coort

doi:10.1016/B978-0-323-91386-7.00041-6

Pathway based-analysis of transcriptomic data from vitamin D studies

Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic

Abstract

Nutritional systems biology is an evolving research field aimed at understanding nutritional processes at the systems level. Combining the effects of nutritional compounds on gene expression with information about expression regulation can shed new light on the action mechanism. Nowadays, pathway-based approaches are commonly used to understand such regulatory effects of nutrients. In this chapter, the key bioinformatics methods and tools for pathway-based analysis will be discussed, with a focus on vitamin D research. The six different steps in the analysis workflow and their purpose will be described in detail. Thereafter, the workflow will be demonstrated with a use case that investigates the effect of 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) on immune cells.

Original language	English
Title of host publication	Feldman and Pike's Vitamin D: Volume One: Biochemistry, Physiology and Diagnostics
Publisher	Elsevier
Pages	291-299
Number of pages	9
ISBN (Electronic)	9780323913867
ISBN (Print)	9780323913904
DOIs	https://doi.org/10.1016/B978-0-323-91386-7.00041-6
Publication status	Published - 1 Jan 2023

Keywords

Enrichment analysis
Immune cells
Networks
Pathways
Transcriptomicdata
Visualization

Access to Document

10.1016/B978-0-323-91386-7.00041-6

Cite this

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title = "Pathway based-analysis of transcriptomic data from vitamin D studies",

abstract = "Nutritional systems biology is an evolving research field aimed at understanding nutritional processes at the systems level. Combining the effects of nutritional compounds on gene expression with information about expression regulation can shed new light on the action mechanism. Nowadays, pathway-based approaches are commonly used to understand such regulatory effects of nutrients. In this chapter, the key bioinformatics methods and tools for pathway-based analysis will be discussed, with a focus on vitamin D research. The six different steps in the analysis workflow and their purpose will be described in detail. Thereafter, the workflow will be demonstrated with a use case that investigates the effect of 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) on immune cells.",

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AU - Coort, Susan L.M.

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AB - Nutritional systems biology is an evolving research field aimed at understanding nutritional processes at the systems level. Combining the effects of nutritional compounds on gene expression with information about expression regulation can shed new light on the action mechanism. Nowadays, pathway-based approaches are commonly used to understand such regulatory effects of nutrients. In this chapter, the key bioinformatics methods and tools for pathway-based analysis will be discussed, with a focus on vitamin D research. The six different steps in the analysis workflow and their purpose will be described in detail. Thereafter, the workflow will be demonstrated with a use case that investigates the effect of 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) on immune cells.

KW - Enrichment analysis

KW - Immune cells

KW - Networks

KW - Pathways

KW - Transcriptomicdata

KW - Visualization

U2 - 10.1016/B978-0-323-91386-7.00041-6

DO - 10.1016/B978-0-323-91386-7.00041-6

M3 - Chapter

SN - 9780323913904

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EP - 299

BT - Feldman and Pike's Vitamin D: Volume One: Biochemistry, Physiology and Diagnostics

PB - Elsevier

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