EpiRegNet: Constructing epigenetic regulatory network from high throughput gene expression data for humans

Wang, Lily Yan; Wang, Panwen; Plewczynski, Dariusz; Qin, Jin; Wang, Xiaowo; Zhang, Michael Q.; Wang, Junwen

doi:10.4161/epi.6.12.18176

Cited by 19 publications

(11 citation statements)

References 24 publications

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“…We then applied popular feature selection methods, either elastic net 17 or Lasso 18 , to the linear model (1) to filter out redundant or non-significant factors. The estimation of β by elastic net is determined bŷ…”

Section: Workflow Of Nchmr Detectormentioning

confidence: 99%

“…HMCan [12] and ChIPseqR [13] were specially designed to accurately identify genomic loci of HMs, while Epigram [14] and DeepHistone [15] can be used to predict loci of HMs based on sequence features and chromatin accessibility. DeepChrome [16], EpiRegNet [17], and Epidaurus [18] were designed for revealing the regulatory functions of HMs on transcription regulation. However, the aims of the above methods were fundamentally different to the identification of non-classical functions of HMRs.…”

Section: Introductionmentioning

confidence: 99%

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ncHMR detector: a computational framework to systematically reveal non-classical functions of histone modification regulators

Huo

et al. 2020

Genome Biol

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Recently, several non-classical functions of histone modification regulators (HMRs), independent of their known histone modification substrates and products, have been reported to be essential for specific cellular processes. However, there is no framework designed for identifying such functions systematically. Here, we develop ncHMR detector, the first computational framework to predict non-classical functions and cofactors of a given HMR, based on ChIP-seq data mining. We apply ncHMR detector in ChIP-seq data-rich cell types and predict non-classical functions of HMRs. Finally, we experimentally reveal that the predicted non-classical function of CBX7 is biologically significant for the maintenance of pluripotency.

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Section: Workflow Of Nchmr Detectormentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

ncHMR detector: a computational framework to systematically reveal non-classical functions of histone modification regulators

Huo

et al. 2020

Genome Biol

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“…The server also provides network visualization via a user-friendly interface and data can be downloaded in batch mode. The web site is implemented in Perl, PHP, and MySQL and it is compatible with all major browsers [90]. Repitools is a toolbox for interrogating and visualizing epigenomic data.…”

Section: Software and Packagesmentioning

confidence: 99%

Bioinformatics and Biostatistics in Mining Epigenetic Disease Markers and Targets

Zhang

et al. 2015

Epigenetic Technological Applications

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“…For example, EpiRegNet is a publicly available web server that allows the construction of epigenetic regulatory networks from human transcriptomic data (Wang et al, 2011). Another model, the Artificial Epigenetic Regulatory Network (AERN) incorporated DNA methylation and chromatin modification in addition to genetic factors for the analysis of epigenetic networks (Turner et al, 2013).…”

Section: Epigenetics Aging and Neurodegenerative Disordersmentioning

confidence: 99%

Dissecting the Molecular Mechanisms of Neurodegenerative Diseases through Network Biology

Santiago

Bottero

Potashkin

2017

Front. Aging Neurosci.

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Neurodegenerative diseases are rarely caused by a mutation in a single gene but rather influenced by a combination of genetic, epigenetic and environmental factors. Emerging high-throughput technologies such as RNA sequencing have been instrumental in deciphering the molecular landscape of neurodegenerative diseases, however, the interpretation of such large amounts of data remains a challenge. Network biology has become a powerful platform to integrate multiple omics data to comprehensively explore the molecular networks in the context of health and disease. In this review article, we highlight recent advances in network biology approaches with an emphasis in brain-networks that have provided insights into the molecular mechanisms leading to the most prevalent neurodegenerative diseases including Alzheimer’s (AD), Parkinson’s (PD) and Huntington’s diseases (HD). We discuss how integrative approaches using multi-omics data from different tissues have been valuable for identifying biomarkers and therapeutic targets. In addition, we discuss the challenges the field of network medicine faces toward the translation of network-based findings into clinically actionable tools for personalized medicine applications.

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EpiRegNet: Constructing epigenetic regulatory network from high throughput gene expression data for humans

Cited by 19 publications

References 24 publications

ncHMR detector: a computational framework to systematically reveal non-classical functions of histone modification regulators

ncHMR detector: a computational framework to systematically reveal non-classical functions of histone modification regulators

Bioinformatics and Biostatistics in Mining Epigenetic Disease Markers and Targets

Dissecting the Molecular Mechanisms of Neurodegenerative Diseases through Network Biology

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