ReviewJournal of advanced research2025
Unlocking biological insights from differentially expressed genes: Concepts, methods, and future perspectives.
Review in Journal of advanced research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed.
- Article
- Physiological and transcriptomic analyses reveal HuBBX1 activating the transcription of COR genes to enhance pitaya cold tolerance.Plant cell reports · 2026Article
- Replacing fish oil with Tetraselmis chui microalgae biomass does not compromise rainbow trout health: Biochemical, histologic, antioxidant and immune gene expression.Scientific reports · 2026Article
- From Laboratory to Patient Access: A Scoping Review of the Multi-Dimensional Challenges in Drug Repurposing.Pharmacy (Basel, Switzerland) · 2026Review
- Transcriptomic Evidence of Immune-Tumor Uncoupling Defines a High-Risk State in Uterine Corpus Endometrial Carcinoma.International journal of molecular sciences · 2026Article
- Multiomics Analysis across the Life Cycle Identifies ZnJournal of agricultural and food chemistry · 2026Article
- Review
- Multi-Scale Transcriptomics Redefining the Tumor Immune Microenvironment.Biotech (Basel (Switzerland)) · 2026Review
- Mechanistic insights into daidzin from Glycine max against breast cancer via network pharmacology and multi-level molecular modeling.PloS one · 2026Article
- Comparative transcriptome analysis reveals cadmium tolerance mechanisms in twoFrontiers in plant science · 2026Article
- Article
- Article
- Comparative Genomics, Transcriptome, and Prokaryotic Expression Analysis ofInternational journal of molecular sciences · 2025Article
- Alterations in Gene Expression and Alternative Splicing Induced by Plasmid-Mediated Overexpression of GFP andInternational journal of molecular sciences · 2025Article
- Integrative transcriptomic analysis reveals microglial metabolic-inflammatory crosstalk of HK2-HSPA5-TNF axis after intracerebral hemorrhage.Frontiers in bioinformatics · 2025Article
- Comparative Analysis of ICS Combined with LABA versus Addition of Omalizumab on Transcriptomic Expression Profiles in Patients with Allergic Asthma.Journal of asthma and allergy · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIdentifying differentially expressed genes (DEGs) is a core task of transcriptome analysis, as DEGs can reveal the molecular mechanisms underlying biological processes. However, interpreting the biological significance of large DEG lists is challenging. Currently, gene ontology, pathway enrichment and protein-protein interaction analysis are common strategies employed by biologists. Additionally, emerging analytical strategies/approaches (such as network module analysis, knowledge graph, drug repurposing, cell marker discovery, trajectory analysis, and cell communication analysis) have been proposed. Despite these advances, comprehensive guidelines for systematically and thoroughly mining the biological information within DEGs remain lacking. AIM OF REVIEW: This review aims to provide an overview of essential concepts and methodologies for the biological interpretation of DEGs, enhancing the contextual understanding. It also addresses the current limitations and future perspectives of these approaches, highlighting their broad applications in deciphering the molecular mechanism of complex diseases and phenotypes. To assist users in extracting insights from extensive datasets, especially various DEG lists, we developed DEGMiner (https://www.ciblab.net/DEGMiner/), which integrates over 300 easily accessible databases and tools. KEY SCIENTIFIC CONCEPTS OF REVIEW: This review offers strong support and guidance for exploring DEGs, and also will accelerate the discovery of hidden biological insights within genomes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.