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The architecture of the gene regulatory networks of different tissues

Summary: The great variety of human cell types in morphology and function is due to the diverse gene expression profiles that are governed by the distinctive regulatory networks in different cell types. It is still a challenging task to explain how the regulatory networks achieve the diversity of di...

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Autores principales: Li, Jie, Hua, Xu, Haubrock, Martin, Wang, Jin, Wingender, Edgar
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436814/
https://www.ncbi.nlm.nih.gov/pubmed/22962474
http://dx.doi.org/10.1093/bioinformatics/bts387
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author Li, Jie
Hua, Xu
Haubrock, Martin
Wang, Jin
Wingender, Edgar
author_facet Li, Jie
Hua, Xu
Haubrock, Martin
Wang, Jin
Wingender, Edgar
author_sort Li, Jie
collection PubMed
description Summary: The great variety of human cell types in morphology and function is due to the diverse gene expression profiles that are governed by the distinctive regulatory networks in different cell types. It is still a challenging task to explain how the regulatory networks achieve the diversity of different cell types. Here, we report on our studies of the design principles of the tissue regulatory system by constructing the regulatory networks of eight human tissues, which subsume the regulatory interactions between transcription factors (TFs), microRNAs (miRNAs) and non-TF target genes. The results show that there are in-/out-hubs of high in-/out-degrees in tissue networks. Some hubs (strong hubs) maintain the hub status in all the tissues where they are expressed, whereas others (weak hubs), in spite of their ubiquitous expression, are hubs only in some tissues. The network motifs are mostly feed-forward loops. Some of them having no miRNAs are the common motifs shared by all tissues, whereas the others containing miRNAs are the tissue-specific ones owned by one or several tissues, indicating that the transcriptional regulation is more conserved across tissues than the post-transcriptional regulation. In particular, a common bow-tie framework was found that underlies the motif instances and shows diverse patterns in different tissues. Such bow-tie framework reflects the utilization efficiency of the regulatory system as well as its high variability in different tissues, and could serve as the model to further understand the structural adaptation of the regulatory system to the specific requirements of different cell functions. Contact: edgar.wingender@bioinf.med.uni-goettingen.de; jwang@nju.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.
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spelling pubmed-34368142012-12-12 The architecture of the gene regulatory networks of different tissues Li, Jie Hua, Xu Haubrock, Martin Wang, Jin Wingender, Edgar Bioinformatics Original Papers Summary: The great variety of human cell types in morphology and function is due to the diverse gene expression profiles that are governed by the distinctive regulatory networks in different cell types. It is still a challenging task to explain how the regulatory networks achieve the diversity of different cell types. Here, we report on our studies of the design principles of the tissue regulatory system by constructing the regulatory networks of eight human tissues, which subsume the regulatory interactions between transcription factors (TFs), microRNAs (miRNAs) and non-TF target genes. The results show that there are in-/out-hubs of high in-/out-degrees in tissue networks. Some hubs (strong hubs) maintain the hub status in all the tissues where they are expressed, whereas others (weak hubs), in spite of their ubiquitous expression, are hubs only in some tissues. The network motifs are mostly feed-forward loops. Some of them having no miRNAs are the common motifs shared by all tissues, whereas the others containing miRNAs are the tissue-specific ones owned by one or several tissues, indicating that the transcriptional regulation is more conserved across tissues than the post-transcriptional regulation. In particular, a common bow-tie framework was found that underlies the motif instances and shows diverse patterns in different tissues. Such bow-tie framework reflects the utilization efficiency of the regulatory system as well as its high variability in different tissues, and could serve as the model to further understand the structural adaptation of the regulatory system to the specific requirements of different cell functions. Contact: edgar.wingender@bioinf.med.uni-goettingen.de; jwang@nju.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2012-09-15 2012-09-03 /pmc/articles/PMC3436814/ /pubmed/22962474 http://dx.doi.org/10.1093/bioinformatics/bts387 Text en © The Author(s) (2012). Published by Oxford University Press. 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 work is properly cited.
spellingShingle Original Papers
Li, Jie
Hua, Xu
Haubrock, Martin
Wang, Jin
Wingender, Edgar
The architecture of the gene regulatory networks of different tissues
title The architecture of the gene regulatory networks of different tissues
title_full The architecture of the gene regulatory networks of different tissues
title_fullStr The architecture of the gene regulatory networks of different tissues
title_full_unstemmed The architecture of the gene regulatory networks of different tissues
title_short The architecture of the gene regulatory networks of different tissues
title_sort architecture of the gene regulatory networks of different tissues
topic Original Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436814/
https://www.ncbi.nlm.nih.gov/pubmed/22962474
http://dx.doi.org/10.1093/bioinformatics/bts387
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