Biocontrol Gene Discovery in Microorganisms by Transcription Profiling

Published: Jan. 1, 2025

Language: Английский

---

Bibliometric Analysis on Methods and Tools Developed for DGE Analysis: Current Trends and Future Perspectives

Yüzüncü Yıl Üniversitesi Fen Bilimleri Enstitüsü Dergisi, Journal Year: 2025, Volume and Issue: 30(1), P. 78 - 91

Published: April 28, 2025

Differential gene expression (DGE) analysis has gained significant attention with the advent of next-generation sequencing technologies, leading to development a wide range methods and tools for DGE analysis. We performed bibliometric using Biblioshiny VOSviewer software investigate trends over investigated period. Relevant papers differential related terms as subjects from 2005 2023 were retrieved Web Science database. Network maps generated illustrate published A total 729 studies examined reveal in methodologies, tools, packages. In analysis, co-authorship, bibliographic coupling, co-occurrence analyses conducted country, institution, source, author, keyword productivity. It was found that output citation numbers increased after 2005. During study period, USA China emerged contributors field. The temporal revealed increase publications at certain times, followed by period slight decrease. greatest fall observed between 2008 2010. Despite these decreases, remains critical topic genomics due its essential role understanding mechanisms any disease, function, therapeutic targets. This trend suggests current are considered sufficiently powerful identifying key informative genes associated diverse diseases.

Language: Английский

---

Polyploidy Promotes Hypertranscription, Apoptosis Resistance, and Ciliogenesis in Cancer Cells and Mesenchymal Stem Cells of Various Origins: Comparative Transcriptome In Silico Study

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(8), P. 4185 - 4185

Published: April 10, 2024

Mesenchymal stem cells (MSC) attract an increasing amount of attention due to their unique therapeutic properties. Yet, MSC can undergo undesirable genetic and epigenetic changes during propagation in vitro. In this study, we investigated whether polyploidy compromise oncological safety For purpose, compared the impact on transcriptome cancer various origins (bone marrow, placenta, heart). First, identified genes that are consistently ploidy-induced or ploidy-repressed through all comparisons. Then, selected master regulators using protein interaction enrichment analysis (PIEA). The obtained ploidy-related gene signatures were verified data gained from polyploid diploid populations early cardiomyocytes (CARD) originating iPSC. multistep bioinformatic applied cells, MSC, CARD indicated plays a pivotal role driving cell into hypertranscription. It was evident upregulation modules implicated housekeeping functions, stemness, unicellularity, DNA repair, chromatin opening by means histone acetylation operating via damage associated with NUA4/TIP60 complex. These features complemented activation pathways centrosome maintenance ciliogenesis impairment related apoptosis, circadian clock, immunity. Overall, our findings suggest that, although does not induce oncologic transformation it might properties because global alterations fundamental biological processes. results contribute development implementation approaches enhancing removing population.

Language: Английский

---

Deciphering Teixobactin Resistance Mechanisms in Enterococcus faecalis Through Integrated RNA-seq and Hub Genes Identification

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: May 2, 2024

Antimicrobial resistance (AMR) poses a severe and pressing global health crisis, necessitating urgent innovative approaches to combat drug-resistant bacteria. This study investigates the genetic underpinnings of in Enterococcus faecalis., Gram-positive bacterium, response novel antibiotic Teixobactin. Leveraging whole transcriptome RNA-seq analysis sophisticated bioinformatics tools, we have identified ten central hub genes: guaA, guaB, lepA, der, secA, ftsH, obg, nusG, dnaA, ffh. These genes display significant upregulation robust interactions within bacterial genome. Our comprehensive uncovers involvement these diverse critical cellular functions associated with resistance. encompass purine metabolism, protein export, stress response, transcriptional regulation, ribosomal activities. findings provide crucial insights into intricate molecular mechanisms underpinning Enterococcus faecalis Furthermore, potential targets were for development advanced antibiotics, aligning ongoing efforts against Resistance (AMR), offer promising avenues drug discovery, bolstering crusade infections.

Language: Английский

---

Tools and Databases in Transcriptomics Analysis: Recent Knowledge and Advancements

Elsevier eBooks, Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 1, 2024

Language: Английский

---