Processing and quality control of DNA array hybridization data

T. Beißbarth; K. Fellenberg; B. Brors; R. Arribas-Prat; J. M. Boer; N. C. Hauser; M. Scheideler; J. D. Hoheisel; G. Schütz; A. Poustka; M. Vingron

doi:10.1093/bioinformatics/16.11.1014

Processing and quality control of DNA array hybridization data

T. Beißbarth
, K. Fellenberg
, B. Brors
, R. Arribas-Prat
, J. M. Boer
, N. C. Hauser
, M. Scheideler
, J. D. Hoheisel
, G. Schütz
, A. Poustka
, M. Vingron

Research output: Contribution to journal › Article › peer-review

117 Citations (Scopus)

Abstract

Motivation: The technology of hybridization to DNA arrays is used to obtain the expression levels of many different genes simultaneously. It enables searching for genes that are expressed specifically under certain conditions. However, the technology produces large amounts of data demanding computational methods for their analysis. It is necessary to find ways to compare data from different experiments and to consider the quality and reproducibility of the data. Results: Data analyzed in this paper have been generated by hybridization of radioactively labeled targets to DNA arrays spotted on nylon membranes. We introduce methods to compare the intensity values of several hybridization experiments. This is essential to find differentially expressed genes or to do pattern analysis. We also discuss possibilities for quality control of the acquired data.

Original language	English
Pages (from-to)	1014-1022
Number of pages	9
Journal	Bioinformatics
Volume	16
Issue number	11
DOIs	https://doi.org/10.1093/bioinformatics/16.11.1014
Publication status	Published - 2000
Externally published	Yes

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10.1093/bioinformatics/16.11.1014

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title = "Processing and quality control of DNA array hybridization data",

abstract = "Motivation: The technology of hybridization to DNA arrays is used to obtain the expression levels of many different genes simultaneously. It enables searching for genes that are expressed specifically under certain conditions. However, the technology produces large amounts of data demanding computational methods for their analysis. It is necessary to find ways to compare data from different experiments and to consider the quality and reproducibility of the data. Results: Data analyzed in this paper have been generated by hybridization of radioactively labeled targets to DNA arrays spotted on nylon membranes. We introduce methods to compare the intensity values of several hybridization experiments. This is essential to find differentially expressed genes or to do pattern analysis. We also discuss possibilities for quality control of the acquired data.",

author = "T. Bei{\ss}barth and K. Fellenberg and B. Brors and R. Arribas-Prat and Boer, \{J. M.\} and Hauser, \{N. C.\} and M. Scheideler and Hoheisel, \{J. D.\} and G. Sch{\"u}tz and A. Poustka and M. Vingron",

note = "Funding Information: We gladly acknowledge the following people for their help, discussions or suggestions: Rainer Spang, Tobias M{\"u}ller, Richard Desper, Bernhard Korn, Hilmar Lapp (Novartis) and Maja Vujic. The presented work was carried out at the DKFZ, Department of Theoretical Bioinformatics. Data were generated at the Departments of Molecular Cell Biology I headed by G{\"u}nther Sch{\"u}tz, Functional Genome Analysis headed by J{\"o}rg Hoheisel and Molecular Genome Analysis headed by Annemarie Poustka. Work was funded by the Deutsche Forschungs-gemeinschaft, the Bundesministerium f{\"u}r Bildung und Forschung, and by the European Commission.",

year = "2000",

doi = "10.1093/bioinformatics/16.11.1014",

language = "English",

volume = "16",

pages = "1014--1022",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "11",

}

TY - JOUR

T1 - Processing and quality control of DNA array hybridization data

AU - Beißbarth, T.

AU - Fellenberg, K.

AU - Brors, B.

AU - Arribas-Prat, R.

AU - Boer, J. M.

AU - Hauser, N. C.

AU - Scheideler, M.

AU - Hoheisel, J. D.

AU - Schütz, G.

AU - Poustka, A.

AU - Vingron, M.

N1 - Funding Information: We gladly acknowledge the following people for their help, discussions or suggestions: Rainer Spang, Tobias Müller, Richard Desper, Bernhard Korn, Hilmar Lapp (Novartis) and Maja Vujic. The presented work was carried out at the DKFZ, Department of Theoretical Bioinformatics. Data were generated at the Departments of Molecular Cell Biology I headed by Günther Schütz, Functional Genome Analysis headed by Jörg Hoheisel and Molecular Genome Analysis headed by Annemarie Poustka. Work was funded by the Deutsche Forschungs-gemeinschaft, the Bundesministerium für Bildung und Forschung, and by the European Commission.

PY - 2000

Y1 - 2000

N2 - Motivation: The technology of hybridization to DNA arrays is used to obtain the expression levels of many different genes simultaneously. It enables searching for genes that are expressed specifically under certain conditions. However, the technology produces large amounts of data demanding computational methods for their analysis. It is necessary to find ways to compare data from different experiments and to consider the quality and reproducibility of the data. Results: Data analyzed in this paper have been generated by hybridization of radioactively labeled targets to DNA arrays spotted on nylon membranes. We introduce methods to compare the intensity values of several hybridization experiments. This is essential to find differentially expressed genes or to do pattern analysis. We also discuss possibilities for quality control of the acquired data.

AB - Motivation: The technology of hybridization to DNA arrays is used to obtain the expression levels of many different genes simultaneously. It enables searching for genes that are expressed specifically under certain conditions. However, the technology produces large amounts of data demanding computational methods for their analysis. It is necessary to find ways to compare data from different experiments and to consider the quality and reproducibility of the data. Results: Data analyzed in this paper have been generated by hybridization of radioactively labeled targets to DNA arrays spotted on nylon membranes. We introduce methods to compare the intensity values of several hybridization experiments. This is essential to find differentially expressed genes or to do pattern analysis. We also discuss possibilities for quality control of the acquired data.

UR - https://www.scopus.com/pages/publications/0034518156

U2 - 10.1093/bioinformatics/16.11.1014

DO - 10.1093/bioinformatics/16.11.1014

M3 - Article

C2 - 11159313

AN - SCOPUS:0034518156

SN - 1367-4803

VL - 16

SP - 1014

EP - 1022

JO - Bioinformatics

JF - Bioinformatics

IS - 11

ER -

Processing and quality control of DNA array hybridization data

Abstract

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