Genetic susceptibility for periodontitis with special focus on immune-related genes: A concise review

Sayad, Arezou; Gholami, Leila; Mirzajani, Sara; Omrani, Mir Davood; Ghafouri‐Fard, Soudeh

doi:10.1016/j.genrep.2020.100814

Cited by 5 publications

(1 citation statement)

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“…Given the pivotal role of Tenm2 in neuronal cells, its transcriptional products exhibit a biased expression primarily in the central nervous system, brain, and other neuralrelated tissues as demonstrated by Mouse ENCODE transcriptome data (Yue et al, 2014). Although gene Tenm2 has been reported to be associated with diseases such as periodontitis and anosmia (Alkelai et al, 2016;Sayad et al, 2020), the linkage between Tenm2 and diseases was primarily built on the basis of genomic studies. Our analysis highlighted the epigenetic modification on gene regulation, indicating that chromatin accessibility at the gene region plays a crucial role in the selective expression of genes, which can serve as cell type-specific markers.…”

Section: Figurementioning

confidence: 99%

Characterization of chromatin accessibility patterns in different mouse cell types using machine learning methods at single-cell resolution

Huang

Guo

et al. 2023

Front. Genet.

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Chromatin accessibility is a generic property of the eukaryotic genome, which refers to the degree of physical compaction of chromatin. Recent studies have shown that chromatin accessibility is cell type dependent, indicating chromatin heterogeneity across cell lines and tissues. The identification of markers used to distinguish cell types at the chromosome level is important to understand cell function and classify cell types. In the present study, we investigated transcriptionally active chromosome segments identified by sci-ATAC-seq at single-cell resolution, including 69,015 cells belonging to 77 different cell types. Each cell was represented by existence status on 20,783 genes that were obtained from 436,206 active chromosome segments. The gene features were deeply analyzed by Boruta, resulting in 3897 genes, which were ranked in a list by Monte Carlo feature selection. Such list was further analyzed by incremental feature selection (IFS) method, yielding essential genes, classification rules and an efficient random forest (RF) classifier. To improve the performance of the optimal RF classifier, its features were further processed by autoencoder, light gradient boosting machine and IFS method. The final RF classifier with MCC of 0.838 was constructed. Some marker genes such as H2-Dmb2, which are specifically expressed in antigen-presenting cells (e.g., dendritic cells or macrophages), and Tenm2, which are specifically expressed in T cells, were identified in this study. Our analysis revealed numerous potential epigenetic modification patterns that are unique to particular cell types, thereby advancing knowledge of the critical functions of chromatin accessibility in cell processes.

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Section: Figurementioning

confidence: 99%