Cargando…
Detecting protein complexes from active protein interaction networks constructed with dynamic gene expression profiles
BACKGROUND: Protein interaction networks (PINs) are known to be useful to detect protein complexes. However, most available PINs are static, which cannot reflect the dynamic changes in real networks. At present, some researchers have tried to construct dynamic networks by incorporating time-course (...
Autores principales: | , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3908890/ https://www.ncbi.nlm.nih.gov/pubmed/24565281 http://dx.doi.org/10.1186/1477-5956-11-S1-S20 |
_version_ | 1782301760170229760 |
---|---|
author | Xiao, Qianghua Wang, Jianxin Peng, Xiaoqing Wu, Fang-Xiang |
author_facet | Xiao, Qianghua Wang, Jianxin Peng, Xiaoqing Wu, Fang-Xiang |
author_sort | Xiao, Qianghua |
collection | PubMed |
description | BACKGROUND: Protein interaction networks (PINs) are known to be useful to detect protein complexes. However, most available PINs are static, which cannot reflect the dynamic changes in real networks. At present, some researchers have tried to construct dynamic networks by incorporating time-course (dynamic) gene expression data with PINs. However, the inevitable background noise exists in the gene expression array, which could degrade the quality of dynamic networkds. Therefore, it is needed to filter out contaminated gene expression data before further data integration and analysis. RESULTS: Firstly, we adopt a dynamic model-based method to filter noisy data from dynamic expression profiles. Then a new method is proposed for identifying active proteins from dynamic gene expression profiles. An active protein at a time point is defined as the protein the expression level of whose corresponding gene at that time point is higher than a threshold determined by a standard variance involved threshold function. Furthermore, a noise-filtered active protein interaction network (NF-APIN) is constructed. To demonstrate the efficiency of our method, we detect protein complexes from the NF-APIN, compared with those from other dynamic PINs. CONCLUSION: A dynamic model based method can effectively filter out noises in dynamic gene expression data. Our method to compute a threshold for determining the active time points of noise-filtered genes can make the dynamic construction more accuracy and provide a high quality framework for network analysis, such as protein complex prediction. |
format | Online Article Text |
id | pubmed-3908890 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-39088902014-02-13 Detecting protein complexes from active protein interaction networks constructed with dynamic gene expression profiles Xiao, Qianghua Wang, Jianxin Peng, Xiaoqing Wu, Fang-Xiang Proteome Sci Research BACKGROUND: Protein interaction networks (PINs) are known to be useful to detect protein complexes. However, most available PINs are static, which cannot reflect the dynamic changes in real networks. At present, some researchers have tried to construct dynamic networks by incorporating time-course (dynamic) gene expression data with PINs. However, the inevitable background noise exists in the gene expression array, which could degrade the quality of dynamic networkds. Therefore, it is needed to filter out contaminated gene expression data before further data integration and analysis. RESULTS: Firstly, we adopt a dynamic model-based method to filter noisy data from dynamic expression profiles. Then a new method is proposed for identifying active proteins from dynamic gene expression profiles. An active protein at a time point is defined as the protein the expression level of whose corresponding gene at that time point is higher than a threshold determined by a standard variance involved threshold function. Furthermore, a noise-filtered active protein interaction network (NF-APIN) is constructed. To demonstrate the efficiency of our method, we detect protein complexes from the NF-APIN, compared with those from other dynamic PINs. CONCLUSION: A dynamic model based method can effectively filter out noises in dynamic gene expression data. Our method to compute a threshold for determining the active time points of noise-filtered genes can make the dynamic construction more accuracy and provide a high quality framework for network analysis, such as protein complex prediction. BioMed Central 2013-11-07 /pmc/articles/PMC3908890/ /pubmed/24565281 http://dx.doi.org/10.1186/1477-5956-11-S1-S20 Text en Copyright © 2013 Xiao et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Xiao, Qianghua Wang, Jianxin Peng, Xiaoqing Wu, Fang-Xiang Detecting protein complexes from active protein interaction networks constructed with dynamic gene expression profiles |
title | Detecting protein complexes from active protein interaction networks constructed with dynamic gene expression profiles |
title_full | Detecting protein complexes from active protein interaction networks constructed with dynamic gene expression profiles |
title_fullStr | Detecting protein complexes from active protein interaction networks constructed with dynamic gene expression profiles |
title_full_unstemmed | Detecting protein complexes from active protein interaction networks constructed with dynamic gene expression profiles |
title_short | Detecting protein complexes from active protein interaction networks constructed with dynamic gene expression profiles |
title_sort | detecting protein complexes from active protein interaction networks constructed with dynamic gene expression profiles |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3908890/ https://www.ncbi.nlm.nih.gov/pubmed/24565281 http://dx.doi.org/10.1186/1477-5956-11-S1-S20 |
work_keys_str_mv | AT xiaoqianghua detectingproteincomplexesfromactiveproteininteractionnetworksconstructedwithdynamicgeneexpressionprofiles AT wangjianxin detectingproteincomplexesfromactiveproteininteractionnetworksconstructedwithdynamicgeneexpressionprofiles AT pengxiaoqing detectingproteincomplexesfromactiveproteininteractionnetworksconstructedwithdynamicgeneexpressionprofiles AT wufangxiang detectingproteincomplexesfromactiveproteininteractionnetworksconstructedwithdynamicgeneexpressionprofiles |