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TTCA: an R package for the identification of differentially expressed genes in time course microarray data

Albrecht, Marco ; Stichel, Damian ; Müller, Benedikt ; Merkle, Ruth ; Sticht, Carsten ; Gretz, Norbert ; Klingmüller, Ursula ; Breuhahn, Kai ; Matthäus, Franziska

In: BMC Bioinformatics, 18 (2017), Nr. 33. pp. 1-11. ISSN 1471-2105

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Download (1MB) | Lizenz: Creative Commons LizenzvertragTTCA: an R package for the identification of differentially expressed genes in time course microarray data by Albrecht, Marco ; Stichel, Damian ; Müller, Benedikt ; Merkle, Ruth ; Sticht, Carsten ; Gretz, Norbert ; Klingmüller, Ursula ; Breuhahn, Kai ; Matthäus, Franziska underlies the terms of Creative Commons Attribution 3.0 Germany

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Abstract

Background: The analysis of microarray time series promises a deeper insight into the dynamics of the cellular response following stimulation. A common observation in this type of data is that some genes respond with quick, transient dynamics, while other genes change their expression slowly over time. The existing methods for detecting significant expression dynamics often fail when the expression dynamics show a large heterogeneity. Moreover, these methods often cannot cope with irregular and sparse measurements. Results: The method proposed here is specifically designed for the analysis of perturbation responses. It combines different scores to capture fast and transient dynamics as well as slow expression changes, and performs well in the presence of low replicate numbers and irregular sampling times. The results are given in the form of tables including links to figures showing the expression dynamics of the respective transcript. These allow to quickly recognise the relevance of detection, to identify possible false positives and to discriminate early and late changes in gene expression. An extension of the method allows the analysis of the expression dynamics of functional groups of genes, providing a quick overview of the cellular response. The performance of this package was tested on microarray data derived from lung cancer cells stimulated with epidermal growth factor (EGF). Conclusion: Here we describe a new, efficient method for the analysis of sparse and heterogeneous time course data with high detection sensitivity and transparency. It is implemented as R package TTCA (transcript time course analysis) and can be installed from the Comprehensive R Archive Network, CRAN. The source code is provided with the Additional file 1.

Item Type: Article
Journal or Publication Title: BMC Bioinformatics
Volume: 18
Number: 33
Publisher: BioMed Central; Springer
Place of Publication: London; Berlin; Heidelberg
Date Deposited: 16 Jan 2017 10:41
Date: 2017
ISSN: 1471-2105
Page Range: pp. 1-11
Faculties / Institutes: Medizinische Fakultät Mannheim > Zentrum für Medizinische Forschung
Service facilities > Interdisciplinary Center for Scientific Computing
Service facilities > German Cancer Research Center (DKFZ)
Medizinische Fakultät Heidelberg > Pathologisches Institut
Subjects: 004 Data processing Computer science
570 Life sciences
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