Article

A Context-Specific, Literature-Supported Framework for Validating Stress Response Differentially Expressed Gene Sets

2025-12-12

Abstract excerpt

<h4>ABSTRACT</h4> Computational models of stress responses identify genes underlying physiological adaptation, but their utility depends on rigorous validation. Often, gene activity reflects both adaptive mechanisms and noise. Here, we develop a framework that leverages public databases to support the subselection of biologically supported model genes for temperature-stress responses. We test our framework on a m...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: 0c339a99-6660-5317-b9ef-4548e92c9450
DOI: 10.64898/2025.12.10.693541

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

A Context-Specific, Literature-Supported Framework for Validating Stress Response Differentially Expressed Gene SetsDOI 10.64898/2025.12.10.693541Read

Genome-Wide Co-Expression Distributions as a Metric to Prioritize Genes of Functional Importance.Semantic proximity Read

Comparative Analysis of Association Networks Using Single-Cell RNA Sequencing Data Reveals Perturbation-Relevant Gene SignaturesSemantic proximity Read

Pathway impact analysis (PIS) for robust and comprehensive interpretation of differentially expressed genes (DEGs)Semantic proximity Read

Comparative Analysis of Association Networks Using Single-Cell RNA Sequencing Data Reveals Perturbation-Relevant Gene SignaturesSemantic proximity Read

Disease-specific interactome alterations via epichaperomics: the case for Alzheimer's disease.Semantic proximity Read

Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean-specific genes.Semantic proximity Read

Fold-change-Specific Enrichment Analysis (FSEA): Quantification of Transcriptional Response Magnitude for Functional Gene GroupsSemantic proximity Read

Gene Expression Network Analysis (GENA) – A Biostatistical Method to Unravel Intricate Relationships Between GenesSemantic proximity Read

Coessential Genetic Networks Reveal the Organization and Constituents of a Dynamic Cellular Stress ResponseSemantic proximity Read

Network perturbation analysis of gene transcriptional profiles reveals protein targets and mechanism of action of drugs and influenza A viral infectionSemantic proximity Read

SLEPR: a sample-level enrichment-based pathway ranking method -- seeking biological themes through pathway-level consistency.Semantic proximity Read

Design principles of gene evolution for niche adaptation through changes in protein-protein interaction networks.Semantic proximity Read