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Bioinformatics tools are imperative for the in depth analysis of heterogeneous high-throughput data. Most of the software tools are developed by specific laboratories or groups or companies wherein they are designed to perform the required analysis for the group. However, such software tools may fail to capture "what the community needs in a tool". Here, we describe a novel community-driven approach to build a comprehensive functional enrichment analysis tool. Using the existing FunRich tool as a template, we invited researchers to request additional features and/or changes. Remarkably, with the enthusiastic participation of the community, we were able to implement 90% of the requested features. FunRich enables plugin for extracellular vesicles wherein users can download and analyse data from Vesiclepedia database. By involving researchers early through community needs software development, we believe that comprehensive analysis tools can be developed in various scientific disciplines.
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http://dx.doi.org/10.1080/20013078.2017.1321455 | DOI Listing |
Med Oncol
September 2025
Division of Hematology and Blood Bank, Department of Medical Laboratory Sciences, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.
Acute Myeloid Leukemia (AML) patient-derived Mesenchymal Stem Cells (MSCs) behave differently than normal ones, creating a more protective environment for leukemia cells, making relapse harder to prevent. This study aimed to identify prognostic biomarkers and elucidate relevant biological pathways in AML by leveraging microarray data and advanced bioinformatics techniques. We retrieved the GSE122917 dataset from the NCBI Gene Expression Omnibus and performed differential expression analysis (DEA) within R Studio to identify differentially expressed genes (DEGs) among healthy donors, newly diagnosed AML patients, and relapsed AML patients.
View Article and Find Full Text PDFMol Biol Rep
September 2025
Phytoveda Pvt. Ltd, Mumbai, 400022, India.
Background: The dysregulation of long-chain noncoding RNAs (lncRNAs) causes several complex human diseases including neurodegenerative disorders across the globe.
Methods And Results: This study aimed to investigate lncRNA expression profiles of Withania somnifera (WS)-treated human neuroblastoma SK-N-SH cells at different timepoints (3 & 9 h) and concentrations (50 & 100 µg/mL) using RNA sequencing. Differential gene expression analysis showed a total of 4772 differentially expressed lncRNAs, out of which 3971 were upregulated and 801 were downregulated compared to controls.
Funct Integr Genomics
September 2025
Department of Plastic Surgery, the First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China.
Keloid scarring and Metabolic Syndrome (MS) are distinct conditions marked by chronic inflammation and tissue dysregulation, suggesting shared pathogenic mechanisms. Identifying common regulatory genes could unveil novel therapeutic targets. Methods.
View Article and Find Full Text PDFFunct Integr Genomics
September 2025
The First Clinical Medical College, Yunnan University of Chinese Medicine, Kunming, China.
Ischemic stroke (IS) has high morbidity/mortality with limited treatments. This study screened core copper homeostasis-related genes in IS and validated their function as precise intervention targets. Human IS gene chip data were retrieved from GEO, and copper homeostasis genes from multiple databases.
View Article and Find Full Text PDFJACC Basic Transl Sci
September 2025
BHF Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom; Department of Pathology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Centre, Maastricht, the Netherlands. Electronic address: andy.bak
Coronary artery bypass graft (CABG) surgery remains the gold standard of care to prevent myocardial ischemia in patients with advanced atherosclerosis; however, poor long-term graft patency remains a considerable and long-standing problem. Excessive vascular smooth muscle cell (SMC) proliferation in the grafted tissue is recognized as central to late CABG failure. We previously identified SMILR, a human-specific SMC-enriched long noncoding RNA that drives SMC proliferation, suggesting that targeting SMILR expression could be a novel way to prevent neointima formation, and thus CABG failure.
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