title: TTCA: an R package for the identification of differentially expressed genes in time course microarray data
creator: Albrecht, Marco
creator: Stichel, Damian
creator: Müller, Benedikt
creator: Merkle, Ruth
creator: Sticht, Carsten
creator: Gretz, Norbert
creator: Klingmüller, Ursula
creator: Breuhahn, Kai
creator: Matthäus, Franziska
subject: 004
subject: 004 Data processing Computer science
subject: 570
subject: 570 Life sciences
description: 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.
publisher: BioMed Central; Springer
date: 2017
type: Article
type: info:eu-repo/semantics/article
type: NonPeerReviewed
format: application/pdf
identifier: https://archiv.ub.uni-heidelberg.de/volltextserverhttps://archiv.ub.uni-heidelberg.de/volltextserver/22488/1/12859_2016_Article_1440.pdf
identifier: DOI:
identifier: urn:nbn:de:bsz:16-heidok-224886
identifier:   Albrecht, Marco ; Stichel, Damian ; Müller, Benedikt ; Merkle, Ruth ; Sticht, Carsten ; Gretz, Norbert ; Klingmüller, Ursula ; Breuhahn, Kai ; Matthäus, Franziska  (2017) TTCA: an R package for the identification of differentially expressed genes in time course microarray data.  BMC Bioinformatics, 18 (33).  pp. 1-11.  ISSN 1471-2105     
relation: https://archiv.ub.uni-heidelberg.de/volltextserver/22488/
rights: info:eu-repo/semantics/openAccess
rights: Please see front page of the work (Sorry, Dublin Core plugin does not recognise license id)
language: eng