Gene Coregulation and Coexpression in the Aryl Hydrocarbon Receptor-mediated Transcriptional Regulatory Network in the Mouse Liver

Josyula, Navya Shilpa; Andersen, Melvin E.; Kaminski, Norbert E.; Dere, Edward; Zacharewski, Timothy R.; Bhattacharya, Sudin

doi:10.1101/260018

Cited by 2 publications

(1 citation statement)

References 56 publications

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“…For example, using over 600 microarray experiments on S. cerevisiae , Allocco et al showed that the correlation ( r ) between any two genes’ expression profile must be over r = 0.84 in order to have a 50% chance of sharing the same regulation by a given transcription factor [57]. Thus, beyond identifying strong correlation between genes’ expression profiles, construction of co-regulation networks requires incorporation of additional regulatory information, which can be provided, for instance, by transcription factor (TF) binding analysis either using in silico databases [58], or including splicing information [59] or chromatin immunoprecipitation (ChIP) data [60]. For example, Ding et al incorporated protein interactions and TF binding motif data to construct gene regulatory networks, identifying ATF1 (Activating Transcription Factor 1), which regulates microglia anti-inflammatory action in AD through the cell surface marker CXCR4 [61,62].…”

Section: Transcriptomic Network To Understand Functional Gene-genmentioning

confidence: 99%

Transcriptional Networks of Microglia in Alzheimer’s Disease and Insights into Pathogenesis

Chew

Petretto

2019

Genes

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Microglia, the main immune cells of the central nervous system, are increasingly implicated in Alzheimer’s disease (AD). Manifold transcriptomic studies in the brain have not only highlighted microglia’s role in AD pathogenesis, but also mapped crucial pathological processes and identified new therapeutic targets. An important component of many of these transcriptomic studies is the investigation of gene expression networks in AD brain, which has provided important new insights into how coordinated gene regulatory programs in microglia (and other cell types) underlie AD pathogenesis. Given the rapid technological advancements in transcriptional profiling, spanning from microarrays to single-cell RNA sequencing (scRNA-seq), tools used for mapping gene expression networks have evolved to keep pace with the unique features of each transcriptomic platform. In this article, we review the trajectory of transcriptomic network analyses in AD from brain to microglia, highlighting the corresponding methodological developments. Lastly, we discuss examples of how transcriptional network analysis provides new insights into AD mechanisms and pathogenesis.

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Section: Transcriptomic Network To Understand Functional Gene-genmentioning

confidence: 99%

Transcriptional Networks of Microglia in Alzheimer’s Disease and Insights into Pathogenesis

Chew

Petretto

2019

Genes

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Role of aryl hydrocarbon receptor in central nervous system tumors: Biological and therapeutic implications (Review)

2021

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Aryl hydrocarbon receptor (AHR) is a ligandactivated transcription factor, whose canonical pathway mainly regulates the genes involved in xenobiotic metabolism. However, it can also regulate several responses in a noncanonical manner, such as proliferation, differentiation, cell death and cell adhesion. AhR plays an important role in central nervous system tumors, as it can regulate several cellular responses via different pathways. The polymorphisms of the AHR gene have been associated with the development of gliomas. In addition, the metabolism of tumor cells promotes tumor growth, particularly in tryptophan synthesis, where some metabolites, such as kynurenine, can activate the AhR pathway, triggering cell proliferation in astrocytomas, medulloblastomas and glioblastomas. Furthermore, as part of the changes in neuroblastomas, AHR is able to downregulate the expression of proto-oncogene c-Myc, induce differentiation in tumor cells, and cause cell cycle arrest and apoptosis. Collectively, these data suggested that the modulation of the AhR pathway may downregulate tumor growth, providing a novel strategy for applications for the treatment of certain tumors through the control of the AhR pathway. Contents

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Gene Coregulation and Coexpression in the Aryl Hydrocarbon Receptor-mediated Transcriptional Regulatory Network in the Mouse Liver

Cited by 2 publications

References 56 publications

Transcriptional Networks of Microglia in Alzheimer’s Disease and Insights into Pathogenesis

Transcriptional Networks of Microglia in Alzheimer’s Disease and Insights into Pathogenesis

Role of aryl hydrocarbon receptor in central nervous system tumors: Biological and therapeutic implications (Review)

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