Universität zu Köln

Seifert, Michael and Beyer, Andreas ORCID: 0000-0002-3891-2123 (2018). regNet: an R package for network-based propagation of gene expression alterations. Bioinformatics, 34 (2). S. 308 - 312. OXFORD: OXFORD UNIV PRESS. ISSN 1460-2059

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Abstract

Gene expression alterations and potentially underlying gene copy number mutations can be measured routinely in the wet lab, but it is still extremely challenging to quantify impacts of altered genes on clinically relevant characteristics to predict putative driver genes. We developed the R package regNet that utilizes gene expression and copy number data to learn regulatory networks for the quantification of potential impacts of individual gene expression alterations on user-defined target genes via network propagation. We demonstrate the value of regNet by identifying putative major regulators that distinguish pilocytic from diffuse astrocytomas and by predicting putative impacts of glioblastoma-specific gene copy number alterations on cell cycle pathway genes and patient survival.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Seifert, Michael UNSPECIFIED UNSPECIFIED UNSPECIFIED Beyer, Andreas UNSPECIFIED orcid.org/0000-0002-3891-2123 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-198858
DOI:	10.1093/bioinformatics/btx544
Journal or Publication Title:	Bioinformatics
Volume:	34
Number:	2
Page Range:	S. 308 - 312
Date:	2018
Publisher:	OXFORD UNIV PRESS
Place of Publication:	OXFORD
ISSN:	1460-2059
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language COPY NUMBER; MUTATIONS; PATHWAYS; LASSO Multiple languages Biochemical Research Methods; Biotechnology & Applied Microbiology; Computer Science, Interdisciplinary Applications; Mathematical & Computational Biology; Statistics & Probability Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/19885