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Network-based inference of master regulators in epithelial membrane protein 2-treated human RPE cells
BACKGROUND: The application of cell-specific construction of transcription regulatory networks (TRNs) to identify their master regulators (MRs) in EMP2 induced vascular proliferation disorders has been largely unexplored. METHODS: Different expression gene (DEGs) analyses was processed with DESeq2 R...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9264685/ https://www.ncbi.nlm.nih.gov/pubmed/35799115 http://dx.doi.org/10.1186/s12863-022-01047-9 |
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author | Wan, Hua Gao, Wei Zhang, Wei Tao, Zijiao Lu, Xiang Chen, Feng Qin, Jian |
author_facet | Wan, Hua Gao, Wei Zhang, Wei Tao, Zijiao Lu, Xiang Chen, Feng Qin, Jian |
author_sort | Wan, Hua |
collection | PubMed |
description | BACKGROUND: The application of cell-specific construction of transcription regulatory networks (TRNs) to identify their master regulators (MRs) in EMP2 induced vascular proliferation disorders has been largely unexplored. METHODS: Different expression gene (DEGs) analyses was processed with DESeq2 R package, for public RNA-seq transcriptome data of EMP2-treated hRPECs versus vector control (VC) or wild type (WT) hRPECs. Virtual Inference of protein activity by Enriched Regulon analysis (VIPER) was used for inferring regulator activity and ARACNE algorithm was conducted to construct TRNs and identify some MRs with DEGs from comparisons. RESULTS: Functional analysis of DEGs and the module analysis of TRNs demonstrated that over-expressed EMP2 leads to a significant induction in the activity of regulators next to transcription factors and other genes implicated in vasculature development, cell proliferation, and protein kinase B signaling, whereas regulators near several genes of platelet activation vascular proliferation were repressed. Among these, PDGFA, ALDH1L2, BA1AP3, ANGPT1 and ST3GAL5 were found differentially expressed and significantly activitve in EMP2-over-expressed hRPECs versus vector control under hypoxia and may thus identified as MRs for EMP2-induced lesion under hypoxia. CONCLUSIONS: MRs obtained in this study might serve as potential biomarkers for EMP2 induced lesion under hypoxia, illustrating gene expression landscapes which might be specific for diabetic retinopathy and might provide improved understanding of the disease. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12863-022-01047-9. |
format | Online Article Text |
id | pubmed-9264685 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-92646852022-07-09 Network-based inference of master regulators in epithelial membrane protein 2-treated human RPE cells Wan, Hua Gao, Wei Zhang, Wei Tao, Zijiao Lu, Xiang Chen, Feng Qin, Jian BMC Genom Data Research BACKGROUND: The application of cell-specific construction of transcription regulatory networks (TRNs) to identify their master regulators (MRs) in EMP2 induced vascular proliferation disorders has been largely unexplored. METHODS: Different expression gene (DEGs) analyses was processed with DESeq2 R package, for public RNA-seq transcriptome data of EMP2-treated hRPECs versus vector control (VC) or wild type (WT) hRPECs. Virtual Inference of protein activity by Enriched Regulon analysis (VIPER) was used for inferring regulator activity and ARACNE algorithm was conducted to construct TRNs and identify some MRs with DEGs from comparisons. RESULTS: Functional analysis of DEGs and the module analysis of TRNs demonstrated that over-expressed EMP2 leads to a significant induction in the activity of regulators next to transcription factors and other genes implicated in vasculature development, cell proliferation, and protein kinase B signaling, whereas regulators near several genes of platelet activation vascular proliferation were repressed. Among these, PDGFA, ALDH1L2, BA1AP3, ANGPT1 and ST3GAL5 were found differentially expressed and significantly activitve in EMP2-over-expressed hRPECs versus vector control under hypoxia and may thus identified as MRs for EMP2-induced lesion under hypoxia. CONCLUSIONS: MRs obtained in this study might serve as potential biomarkers for EMP2 induced lesion under hypoxia, illustrating gene expression landscapes which might be specific for diabetic retinopathy and might provide improved understanding of the disease. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12863-022-01047-9. BioMed Central 2022-07-07 /pmc/articles/PMC9264685/ /pubmed/35799115 http://dx.doi.org/10.1186/s12863-022-01047-9 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Wan, Hua Gao, Wei Zhang, Wei Tao, Zijiao Lu, Xiang Chen, Feng Qin, Jian Network-based inference of master regulators in epithelial membrane protein 2-treated human RPE cells |
title | Network-based inference of master regulators in epithelial membrane protein 2-treated human RPE cells |
title_full | Network-based inference of master regulators in epithelial membrane protein 2-treated human RPE cells |
title_fullStr | Network-based inference of master regulators in epithelial membrane protein 2-treated human RPE cells |
title_full_unstemmed | Network-based inference of master regulators in epithelial membrane protein 2-treated human RPE cells |
title_short | Network-based inference of master regulators in epithelial membrane protein 2-treated human RPE cells |
title_sort | network-based inference of master regulators in epithelial membrane protein 2-treated human rpe cells |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9264685/ https://www.ncbi.nlm.nih.gov/pubmed/35799115 http://dx.doi.org/10.1186/s12863-022-01047-9 |
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