ArticleBioinformatics (Oxford, England)2023
NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
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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.
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Who cites it
24 citing papers in PubMed.
- Epigenetic Insights in Pediatric Multiple Sclerosis: DNA Methylation Highlights an Involvement of Epstein-Barr Virus Infection and Host Immune Networks.Neurology(R) neuroimmunology & neuroinflammation · 2026Article
- GOLDEN fusion: a graph-oriented learning with domain-embedding network fusion for generating super gene sets in functional genomics.Briefings in bioinformatics · 2026Article
- The Gene Ontology knowledgebase in 2026.Nucleic acids research · 2026Article
- Preliminary examination of noncoding mutations of esophageal squamous cell carcinoma in African Americans.Frontiers in genetics · 2026Article
- Proteomic profiling reveals age-related changes in transporter proteins in the human blood-brain barrier.Scientific reports · 2025Article
- Integrating Inflammatory and Epigenetic Signatures in IBD-Associated Colorectal Carcinogenesis: Models, Mechanisms, and Clinical Implications.International journal of molecular sciences · 2025Review
- Article
- LM-Merger: a workflow for merging logical models with an application to gene regulatory network models.BMC bioinformatics · 2025Article
- G-quadruplex structures regulate long-range transcriptional reprogramming to promote drug resistance in ovarian cancer cells.Genome biology · 2025Article
- Cytoscape Web: bringing network biology to the browser.Nucleic acids research · 2025Article
- Single cell transcriptomics in a treatment-segregated cohort exposes a STAT3-regulated therapeutic gap in idiopathic pulmonary fibrosis.bioRxiv : the preprint server for biology · 2025Article
- Transcriptional Landscape and Biomarker Discovery for Endoplasmic Reticulum Stress in Alzheimer's Disease: An Ex Vivo Study Using Patients-Derived Dermal Fibroblasts.Psychiatry investigation · 2025Article
- Extracellular PHF-tau modulates astrocyte mitochondrial dynamics and mediates neuronal connectivity.Translational neurodegeneration · 2025Article
- Unravelling Convergent Signaling Mechanisms Underlying the Aging-Disease Nexus Using Computational Language Analysis.Current issues in molecular biology · 2025Article
- Evaluation of large language models for discovery of gene set function.Nature methods · 2025Article
- Prediction of immunotherapy response using mutations to cancer protein assemblies.Science advances · 2024Article
- Computational prediction of crucial genes involved in gonorrhea infection and neoplastic cell transformation: A multiomics approach.Microbial pathogenesis · 2024Article
- Article
- WikiPathways 2024: next generation pathway database.Nucleic acids research · 2024Article
- Using published pathway figures in enrichment analysis and machine learning.BMC genomics · 2023Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
motivationThe investigation of sets of genes using biological pathways is a common task for researchers and is supported by a wide variety of software tools. This type of analysis generates hypotheses about the biological processes that are active or modulated in a specific experimental context.
resultsThe Network Data Exchange Integrated Query (NDEx IQuery) is a new tool for network and pathway-based gene set interpretation that complements or extends existing resources. It combines novel sources of pathways, integration with Cytoscape, and the ability to store and share analysis results. The NDEx IQuery web application performs multiple gene set analyses based on diverse pathways and networks stored in NDEx. These include curated pathways from WikiPathways and SIGNOR, published pathway figures from the last 27 years, machine-assembled networks using the INDRA system, and the new NCI-PID v2.0, an updated version of the popular NCI Pathway Interaction Database. NDEx IQuery's integration with MSigDB and cBioPortal now provides pathway analysis in the context of these two resources. AVAILABILITY AND IMPLEMENTATION: NDEx IQuery is available at https://www.ndexbio.org/iquery and is implemented in Javascript and Java.
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What OpenQuestion holds
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.