Hi-C, a chromatin 3D structure technique advancing the functional genomics of immune cells
The functional performance of immune cells relies on a complex transcriptional regulatory network. The three-dimensional structure of chromatin can affect chromatin status and gene expression patterns, and plays an important regulatory role in gene transcription. Currently available techniques for studying chromatin spatial structure include chromatin conformation capture techniques and their derivatives, chromatin accessibility sequencing techniques, and others. Additionally, the recently emerged deep learning technology can be utilized as a tool to enhance the analysis of data. In this review, we elucidate the definition...
Source: Frontiers in Genetics - March 22, 2024 Category: Genetics & Stem Cells Source Type: research
Identification of potential biomarkers for idiopathic pulmonary arterial hypertension using single-cell and bulk RNA sequencing analysis
In conclusion, our findings shed light on the pivotal role of arterial endothelial cells in the development of IPAH. Furthermore, the integration of single-cell and bulk RNA sequencing datasets allowed us to pinpoint novel candidate biomarkers for the diagnosis of IPAH. This work opens up new avenues for research and potential therapeutic interventions in IPAH management. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - March 22, 2024 Category: Genetics & Stem Cells Source Type: research
MHIF-MSEA: a novel model of miRNA set enrichment analysis based on multi-source heterogeneous information fusion
Discussion: To determine the optimal network fusion approach, three case studies were introduced: colon cancer, breast cancer, and hepatocellular carcinoma. The experimental results revealed that the miRNA-miRNA association network constructed using miRSN-DA and miRSN-GOA exhibited superior performance as the input network. Furthermore, the MHIF-MSEA model performed enrichment analysis on differentially expressed miRNAs in breast cancer and hepatocellular carcinoma. The achieved p-values were 2.17e(-75) and 1.50e(-77), and the hit rates improved by 39.01% and 44.68% compared to traditional enrichment analysis methods, resp...
Source: Frontiers in Genetics - March 22, 2024 Category: Genetics & Stem Cells Source Type: research
Systemic inflammatory regulators and preeclampsia: a two-sample bidirectional Mendelian randomization study
Conclusion:Our study suggests that SCGF-β, IL-5, IL-9, and TNF-α causally affect the PE risk, while PE is causally associated with MIF. Further studies are needed to validate these biomarkers in managing PE. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - March 22, 2024 Category: Genetics & Stem Cells Source Type: research
Comparative analysis of basal and etoposide-induced alterations in gene expression by DNA-PKcs kinase activity
Conclusion: Overall, our results indicate that DNA-PKcs, in a kinase-dependent fashion, decreases proinflammatory signaling following genotoxic insult. As multiple DNA-PK kinase inhibitors are in clinical trials as cancer therapeutics utilized in combination with DNA damaging agents, understanding the transcriptional response when DNA-PKcs cannot phosphorylate downstream targets will inform the overall patient response to combined treatment. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - March 21, 2024 Category: Genetics & Stem Cells Source Type: research
Editorial: Novel applications of ONT technologies in genomics and transcriptomics
(Source: Frontiers in Genetics)
Source: Frontiers in Genetics - March 20, 2024 Category: Genetics & Stem Cells Source Type: research
A comprehensive analysis of the prognostic characteristics of microRNAs in breast cancer
In conclusion, we thoroughly clarified BC-related miRNAs on DSS and OS and verified miR-551b as a crucial regulator in the development and prognosis of cancer. These results can offer fresh ideas for BC therapy. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - March 20, 2024 Category: Genetics & Stem Cells Source Type: research
Automated recognition of chromosome fusion using an alignment-free natural vector method
Chromosomal fusion is a significant form of structural variation, but research into algorithms for its identification has been limited. Most existing methods rely on synteny analysis, which necessitates manual annotations and always involves inefficient sequence alignments. In this paper, we present a novel alignment-free algorithm for chromosomal fusion recognition. Our method transforms the problem into a series of assignment problems using natural vectors and efficiently solves them with the Kuhn-Munkres algorithm. When applied to the human/gorilla and swamp buffalo/river buffalo datasets, our algorithm successfully and...
Source: Frontiers in Genetics - March 20, 2024 Category: Genetics & Stem Cells Source Type: research
The genetic landscape of autism spectrum disorder in the Middle Eastern population
Conclusion: Despite the ASD multifactorial etiology that hinders ASD genetic risk discovery, the number of identified novel or known putative ASD genetic variants was appreciable. Nevertheless, this study represents the first comprehensive characterization of ASD genetic risk in Qatar's Middle Eastern population. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - March 20, 2024 Category: Genetics & Stem Cells Source Type: research
Gene variants polymorphisms and uterine leiomyoma: an updated review
Uterine leiomyoma, commonly referred to as fibroids, is a benign tumor that develops in the muscular wall of the uterus. These growths are non-cancerous and can vary in size, ranging from tiny nodules to larger masses. Uterine leiomyomas often occur during a woman’s reproductive years and can lead to symptoms such as heavy menstrual bleeding, pelvic pain, and pressure on nearby organs. While the exact cause is not fully understood, hormonal factors, particularly estrogen and progesterone, are believed to play a role in their development. The exploration of connections between genetic variants and uterine leiomyoma has ca...
Source: Frontiers in Genetics - March 20, 2024 Category: Genetics & Stem Cells Source Type: research
Retraction: Corrigendum: The heart of silk road “Xinjiang”, its genetic portray, and forensic parameters inferred from autosomal STRs
(Source: Frontiers in Genetics)
Source: Frontiers in Genetics - March 19, 2024 Category: Genetics & Stem Cells Source Type: research
Retraction: Corrigendum: Cytokinin and abiotic stress tolerance-what has been accomplished and the way forward?
(Source: Frontiers in Genetics)
Source: Frontiers in Genetics - March 19, 2024 Category: Genetics & Stem Cells Source Type: research
Retraction: Cytokinin and abiotic stress tolerance -what has been accomplished and the way forward?
(Source: Frontiers in Genetics)
Source: Frontiers in Genetics - March 19, 2024 Category: Genetics & Stem Cells Source Type: research
Retraction: The heart of silk road “Xinjiang,” its genetic portray, and forensic parameters inferred from autosomal STRs
(Source: Frontiers in Genetics)
Source: Frontiers in Genetics - March 19, 2024 Category: Genetics & Stem Cells Source Type: research
RET splice site variants in medullary thyroid carcinoma
Discussion: The identification of RET SSVs in all MTCs, but rarely in other cancer types, demonstrates that these RET SSVs distinguish MTCs from other cancer types. Future studies are needed to investigate whether these RET SSVs play a pathogenic role in MTC. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - March 19, 2024 Category: Genetics & Stem Cells Source Type: research
