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Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors
The inference of gene regulatory networks gained within recent years a considerable interest in the biology and biomedical community. The purpose of this paper is to investigate the influence that environmental conditions can exhibit on the inference performance of network inference algorithms. Spec...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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PeerJ Inc.
2013
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3628739/ https://www.ncbi.nlm.nih.gov/pubmed/23638344 http://dx.doi.org/10.7717/peerj.10 |
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author | Emmert-Streib, Frank |
author_facet | Emmert-Streib, Frank |
author_sort | Emmert-Streib, Frank |
collection | PubMed |
description | The inference of gene regulatory networks gained within recent years a considerable interest in the biology and biomedical community. The purpose of this paper is to investigate the influence that environmental conditions can exhibit on the inference performance of network inference algorithms. Specifically, we study five network inference methods, Aracne, BC3NET, CLR, C3NET and MRNET, and compare the results for three different conditions: (I) observational gene expression data: normal environmental condition, (II) interventional gene expression data: growth in rich media, (III) interventional gene expression data: normal environmental condition interrupted by a positive spike-in stimulation. Overall, we find that different statistical inference methods lead to comparable, but condition-specific results. Further, our results suggest that non-steady-state data enhance the inferability of regulatory networks. |
format | Online Article Text |
id | pubmed-3628739 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-36287392013-05-01 Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors Emmert-Streib, Frank Peerj Bioinformatics The inference of gene regulatory networks gained within recent years a considerable interest in the biology and biomedical community. The purpose of this paper is to investigate the influence that environmental conditions can exhibit on the inference performance of network inference algorithms. Specifically, we study five network inference methods, Aracne, BC3NET, CLR, C3NET and MRNET, and compare the results for three different conditions: (I) observational gene expression data: normal environmental condition, (II) interventional gene expression data: growth in rich media, (III) interventional gene expression data: normal environmental condition interrupted by a positive spike-in stimulation. Overall, we find that different statistical inference methods lead to comparable, but condition-specific results. Further, our results suggest that non-steady-state data enhance the inferability of regulatory networks. PeerJ Inc. 2013-02-12 /pmc/articles/PMC3628739/ /pubmed/23638344 http://dx.doi.org/10.7717/peerj.10 Text en © 2013 Emmert-Streib http://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Bioinformatics Emmert-Streib, Frank Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors |
title | Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors |
title_full | Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors |
title_fullStr | Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors |
title_full_unstemmed | Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors |
title_short | Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors |
title_sort | influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors |
topic | Bioinformatics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3628739/ https://www.ncbi.nlm.nih.gov/pubmed/23638344 http://dx.doi.org/10.7717/peerj.10 |
work_keys_str_mv | AT emmertstreibfrank influenceoftheexperimentaldesignofgeneexpressionstudiesontheinferenceofgeneregulatorynetworksenvironmentalfactors |