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A bioinformatics workflow to decipher transcriptomic data from vitamin D studies

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A bioinformatics workflow to decipher transcriptomic data from vitamin D studies. / Muñoz García, Amadeo; Eijssen, Lars M; Kutmon, Martina; Sarathy, Chaitra; Cengo, Ardi; Hewison, Martin; Evelo, Chris T; Lenz, Michael; Coort, Susan L.

In: Journal of Steroid Biochemistry and Molecular Biology, Vol. 189, 05.2019, p. 28-35.

Research output: Contribution to journalReview articleAcademicpeer-review

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@article{27de9625ee324d81903edbfe340b2694,
title = "A bioinformatics workflow to decipher transcriptomic data from vitamin D studies",
abstract = "The link between the experimental laboratory studies and bioinformatic approaches aims to find procedures to connect tools from both branches producing workflows that bring together different techniques that are capable of exploiting data at many levels. Thanks to the open access sources and the numerous tools available, it is possible to create various pipelines capable of solving specific problems. Nevertheless the lack of connectivity between them that interconnect different approaches complicates the exploitation of these workflows. Here, we present a detailed description of a workflow composed of different bioinformatics tools that exploits data from large-scale gene expression experiments, contextualizing them at many biological levels. To illustrate the relevance of our workflow for the vitamin D community we applied it to data from myeloid cell models treated with the hormonally active form of vitamin. From raw files of functional genomic studies it is possible to utilize the whole information to obtain a biological insight. Different software and algorithms are included to analyse at pathway, metabolic, ontology and molecular biology level the effects on gene expression. The usage of different databases to analyse gene expression data allows to perform a complete interpretation of functional genomic studies and the implementation of analysis and visualization software tools gives a better understanding of the biological meaning of the results. This review is an example of how to select and bring together several software modules to create one pipeline that processes and analyses genomic data at many biological levels making it open, reproducible and user friendly. Finally, the application of our bioinformatic pipeline revealed that vitamin D modulates crucial metabolic pathways in different myeloid cells that may play an important role in their immune function.",
author = "{Mu{\~n}oz Garc{\'i}a}, Amadeo and Eijssen, {Lars M} and Martina Kutmon and Chaitra Sarathy and Ardi Cengo and Martin Hewison and Evelo, {Chris T} and Michael Lenz and Coort, {Susan L}",
note = "Copyright {\circledC} 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.",
year = "2019",
month = "5",
doi = "10.1016/j.jsbmb.2019.01.003",
language = "English",
volume = "189",
pages = "28--35",
journal = "Journal of Steroid Biochemistry and Molecular Biology",
issn = "0960-0760",
publisher = "Elsevier Science",

}

RIS

TY - JOUR

T1 - A bioinformatics workflow to decipher transcriptomic data from vitamin D studies

AU - Muñoz García, Amadeo

AU - Eijssen, Lars M

AU - Kutmon, Martina

AU - Sarathy, Chaitra

AU - Cengo, Ardi

AU - Hewison, Martin

AU - Evelo, Chris T

AU - Lenz, Michael

AU - Coort, Susan L

N1 - Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.

PY - 2019/5

Y1 - 2019/5

N2 - The link between the experimental laboratory studies and bioinformatic approaches aims to find procedures to connect tools from both branches producing workflows that bring together different techniques that are capable of exploiting data at many levels. Thanks to the open access sources and the numerous tools available, it is possible to create various pipelines capable of solving specific problems. Nevertheless the lack of connectivity between them that interconnect different approaches complicates the exploitation of these workflows. Here, we present a detailed description of a workflow composed of different bioinformatics tools that exploits data from large-scale gene expression experiments, contextualizing them at many biological levels. To illustrate the relevance of our workflow for the vitamin D community we applied it to data from myeloid cell models treated with the hormonally active form of vitamin. From raw files of functional genomic studies it is possible to utilize the whole information to obtain a biological insight. Different software and algorithms are included to analyse at pathway, metabolic, ontology and molecular biology level the effects on gene expression. The usage of different databases to analyse gene expression data allows to perform a complete interpretation of functional genomic studies and the implementation of analysis and visualization software tools gives a better understanding of the biological meaning of the results. This review is an example of how to select and bring together several software modules to create one pipeline that processes and analyses genomic data at many biological levels making it open, reproducible and user friendly. Finally, the application of our bioinformatic pipeline revealed that vitamin D modulates crucial metabolic pathways in different myeloid cells that may play an important role in their immune function.

AB - The link between the experimental laboratory studies and bioinformatic approaches aims to find procedures to connect tools from both branches producing workflows that bring together different techniques that are capable of exploiting data at many levels. Thanks to the open access sources and the numerous tools available, it is possible to create various pipelines capable of solving specific problems. Nevertheless the lack of connectivity between them that interconnect different approaches complicates the exploitation of these workflows. Here, we present a detailed description of a workflow composed of different bioinformatics tools that exploits data from large-scale gene expression experiments, contextualizing them at many biological levels. To illustrate the relevance of our workflow for the vitamin D community we applied it to data from myeloid cell models treated with the hormonally active form of vitamin. From raw files of functional genomic studies it is possible to utilize the whole information to obtain a biological insight. Different software and algorithms are included to analyse at pathway, metabolic, ontology and molecular biology level the effects on gene expression. The usage of different databases to analyse gene expression data allows to perform a complete interpretation of functional genomic studies and the implementation of analysis and visualization software tools gives a better understanding of the biological meaning of the results. This review is an example of how to select and bring together several software modules to create one pipeline that processes and analyses genomic data at many biological levels making it open, reproducible and user friendly. Finally, the application of our bioinformatic pipeline revealed that vitamin D modulates crucial metabolic pathways in different myeloid cells that may play an important role in their immune function.

U2 - 10.1016/j.jsbmb.2019.01.003

DO - 10.1016/j.jsbmb.2019.01.003

M3 - Review article

VL - 189

SP - 28

EP - 35

JO - Journal of Steroid Biochemistry and Molecular Biology

T2 - Journal of Steroid Biochemistry and Molecular Biology

JF - Journal of Steroid Biochemistry and Molecular Biology

SN - 0960-0760

ER -