Publication

Glia Open Access Database (GOAD): A comprehensive gene expression encyclopedia of glia cells in health and disease

Holtman, I. R., Noback, M., Bijlsma, M., Duong, K. N., van der Geest, M. A., Ketelaars, P. T., Brouwer, N., Vainchtein, I. D., Eggen, B. J. L. & Boddeke, H. W. G. M., Sep-2015, In : Glia. 63, 9, p. 1495-1506 12 p.

Research output: Contribution to journalReview articleAcademicpeer-review

APA

Holtman, I. R., Noback, M., Bijlsma, M., Duong, K. N., van der Geest, M. A., Ketelaars, P. T., Brouwer, N., Vainchtein, I. D., Eggen, B. J. L., & Boddeke, H. W. G. M. (2015). Glia Open Access Database (GOAD): A comprehensive gene expression encyclopedia of glia cells in health and disease. Glia, 63(9), 1495-1506. https://doi.org/10.1002/glia.22810

Author

Holtman, Inge R. ; Noback, Michiel ; Bijlsma, Marieke ; Duong, Kim N. ; van der Geest, Marije A. ; Ketelaars, Peer T. ; Brouwer, Nieske ; Vainchtein, Ilia D. ; Eggen, Bart J. L. ; Boddeke, Hendrikus W. G. M. / Glia Open Access Database (GOAD) : A comprehensive gene expression encyclopedia of glia cells in health and disease. In: Glia. 2015 ; Vol. 63, No. 9. pp. 1495-1506.

Harvard

Holtman, IR, Noback, M, Bijlsma, M, Duong, KN, van der Geest, MA, Ketelaars, PT, Brouwer, N, Vainchtein, ID, Eggen, BJL & Boddeke, HWGM 2015, 'Glia Open Access Database (GOAD): A comprehensive gene expression encyclopedia of glia cells in health and disease', Glia, vol. 63, no. 9, pp. 1495-1506. https://doi.org/10.1002/glia.22810

Standard

Glia Open Access Database (GOAD) : A comprehensive gene expression encyclopedia of glia cells in health and disease. / Holtman, Inge R.; Noback, Michiel; Bijlsma, Marieke; Duong, Kim N.; van der Geest, Marije A.; Ketelaars, Peer T.; Brouwer, Nieske; Vainchtein, Ilia D.; Eggen, Bart J. L.; Boddeke, Hendrikus W. G. M.

In: Glia, Vol. 63, No. 9, 09.2015, p. 1495-1506.

Research output: Contribution to journalReview articleAcademicpeer-review

Vancouver

Holtman IR, Noback M, Bijlsma M, Duong KN, van der Geest MA, Ketelaars PT et al. Glia Open Access Database (GOAD): A comprehensive gene expression encyclopedia of glia cells in health and disease. Glia. 2015 Sep;63(9):1495-1506. https://doi.org/10.1002/glia.22810


BibTeX

@article{66d82deead7e48cc92d11ec61704a64b,
title = "Glia Open Access Database (GOAD): A comprehensive gene expression encyclopedia of glia cells in health and disease",
abstract = "Recently, the number of genome-wide transcriptome profiles of pure populations of glia cells has drastically increased, resulting in an unprecedented amount of data that offer opportunities to study glia phenotypes and functions in health and disease. To make genome-wide transcriptome data easily accessible, we developed the Glia Open Access Database (GOAD), available via cation. GOAD contains a collection of previously published and unpublished transcriptome data, including datasets from isolated microglia, astrocytes and oligodendrocytes both at homeostatic and pathological conditions. It contains an intuitive web-based interface that consists of three features that enable searching, browsing, analyzing, and downloading of the data. The first feature is differential gene expression (DE) analysis that provides genes that are significantly up and down-regulated with the associated fold changes and p-values between two conditions of interest. In addition, an interactive Venn diagram is generated to illustrate the overlap and differences between several DE gene lists. The second feature is quantitative gene expression (QE) analysis, to investigate which genes are expressed in a particular glial cell type and to what degree. The third feature is a search utility, which can be used to find a gene of interest and depict its expression in all available expression data sets by generating a gene card. In addition, quality guidelines and relevant concepts for transcriptome analysis are discussed. Finally, GOAD is discussed in relation to several online transcriptome tools developed in neuroscience and immunology. In conclusion, GOAD is a unique platform to facilitate integration of bioinformatics in glia biology. GLIA 2015;63:1495-1506",
keywords = "transcriptome analysis, bioinformatics, RNA-seq, microglia, astrocytes, oligodendrocytes, RNA-SEQ, MICROARRAY DATA, TRANSCRIPTOME, MICROGLIA, BRAIN, ASTROCYTES, SIGNATURE, PROFILES, NEURONS, SYSTEM",
author = "Holtman, {Inge R.} and Michiel Noback and Marieke Bijlsma and Duong, {Kim N.} and {van der Geest}, {Marije A.} and Ketelaars, {Peer T.} and Nieske Brouwer and Vainchtein, {Ilia D.} and Eggen, {Bart J. L.} and Boddeke, {Hendrikus W. G. M.}",
note = "{\textcopyright} 2015 Wiley Periodicals, Inc.",
year = "2015",
month = sep,
doi = "10.1002/glia.22810",
language = "English",
volume = "63",
pages = "1495--1506",
journal = "Glia",
issn = "0894-1491",
publisher = "Wiley",
number = "9",

}

RIS

TY - JOUR

T1 - Glia Open Access Database (GOAD)

T2 - A comprehensive gene expression encyclopedia of glia cells in health and disease

AU - Holtman, Inge R.

AU - Noback, Michiel

AU - Bijlsma, Marieke

AU - Duong, Kim N.

AU - van der Geest, Marije A.

AU - Ketelaars, Peer T.

AU - Brouwer, Nieske

AU - Vainchtein, Ilia D.

AU - Eggen, Bart J. L.

AU - Boddeke, Hendrikus W. G. M.

N1 - © 2015 Wiley Periodicals, Inc.

PY - 2015/9

Y1 - 2015/9

N2 - Recently, the number of genome-wide transcriptome profiles of pure populations of glia cells has drastically increased, resulting in an unprecedented amount of data that offer opportunities to study glia phenotypes and functions in health and disease. To make genome-wide transcriptome data easily accessible, we developed the Glia Open Access Database (GOAD), available via cation. GOAD contains a collection of previously published and unpublished transcriptome data, including datasets from isolated microglia, astrocytes and oligodendrocytes both at homeostatic and pathological conditions. It contains an intuitive web-based interface that consists of three features that enable searching, browsing, analyzing, and downloading of the data. The first feature is differential gene expression (DE) analysis that provides genes that are significantly up and down-regulated with the associated fold changes and p-values between two conditions of interest. In addition, an interactive Venn diagram is generated to illustrate the overlap and differences between several DE gene lists. The second feature is quantitative gene expression (QE) analysis, to investigate which genes are expressed in a particular glial cell type and to what degree. The third feature is a search utility, which can be used to find a gene of interest and depict its expression in all available expression data sets by generating a gene card. In addition, quality guidelines and relevant concepts for transcriptome analysis are discussed. Finally, GOAD is discussed in relation to several online transcriptome tools developed in neuroscience and immunology. In conclusion, GOAD is a unique platform to facilitate integration of bioinformatics in glia biology. GLIA 2015;63:1495-1506

AB - Recently, the number of genome-wide transcriptome profiles of pure populations of glia cells has drastically increased, resulting in an unprecedented amount of data that offer opportunities to study glia phenotypes and functions in health and disease. To make genome-wide transcriptome data easily accessible, we developed the Glia Open Access Database (GOAD), available via cation. GOAD contains a collection of previously published and unpublished transcriptome data, including datasets from isolated microglia, astrocytes and oligodendrocytes both at homeostatic and pathological conditions. It contains an intuitive web-based interface that consists of three features that enable searching, browsing, analyzing, and downloading of the data. The first feature is differential gene expression (DE) analysis that provides genes that are significantly up and down-regulated with the associated fold changes and p-values between two conditions of interest. In addition, an interactive Venn diagram is generated to illustrate the overlap and differences between several DE gene lists. The second feature is quantitative gene expression (QE) analysis, to investigate which genes are expressed in a particular glial cell type and to what degree. The third feature is a search utility, which can be used to find a gene of interest and depict its expression in all available expression data sets by generating a gene card. In addition, quality guidelines and relevant concepts for transcriptome analysis are discussed. Finally, GOAD is discussed in relation to several online transcriptome tools developed in neuroscience and immunology. In conclusion, GOAD is a unique platform to facilitate integration of bioinformatics in glia biology. GLIA 2015;63:1495-1506

KW - transcriptome analysis

KW - bioinformatics

KW - RNA-seq

KW - microglia

KW - astrocytes

KW - oligodendrocytes

KW - RNA-SEQ

KW - MICROARRAY DATA

KW - TRANSCRIPTOME

KW - MICROGLIA

KW - BRAIN

KW - ASTROCYTES

KW - SIGNATURE

KW - PROFILES

KW - NEURONS

KW - SYSTEM

U2 - 10.1002/glia.22810

DO - 10.1002/glia.22810

M3 - Review article

C2 - 25808223

VL - 63

SP - 1495

EP - 1506

JO - Glia

JF - Glia

SN - 0894-1491

IS - 9

ER -

ID: 17592629