ArticleGenome biology2010
Identification of functional modules that correlate with phenotypic difference: the influence of network topology.
Article in Genome biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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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.
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Who cites it
46 citing papers in PubMed.
- Dynamic tracking of functional gene modules in treated juvenile idiopathic arthritis.Genome medicine · 2015Trial
- Reconciling multiple connectivity-based systems biology methods for drug repurposing.Briefings in bioinformatics · 2025Review
- A comprehensive survey of the approaches for pathway analysis using multi-omics data integration.Briefings in bioinformatics · 2022Review
- Review
- VarSAn: associating pathways with a set of genomic variants using network analysis.Nucleic acids research · 2021Article
- Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data.Computational and structural biotechnology journal · 2021Article
- Differential Co-Expression Analyses Allow the Identification of Critical Signalling Pathways Altered during Tumour Transformation and Progression.International journal of molecular sciences · 2020Review
- A framework using topological pathways for deeper analysis of transcriptome data.BMC genomics · 2020Article
- Gene Set Analysis: Challenges, Opportunities, and Future Research.Frontiers in genetics · 2020Review
- Identifying significantly impacted pathways: a comprehensive review and assessment.Genome biology · 2019Review
- A comparison of mechanistic signaling pathway activity analysis methods.Briefings in bioinformatics · 2019Review
- ce-Subpathway: Identification of ceRNA-mediated subpathways via joint power of ceRNAs and pathway topologies.Journal of cellular and molecular medicine · 2019Article
- Article
- Computational systems biology approaches for Parkinson's disease.Cell and tissue research · 2018Review
- Modeling Transcriptional Rewiring in Neutrophils Through the Course of Treated Juvenile Idiopathic Arthritis.Scientific reports · 2018Article
- Model-based analysis of competing-endogenous pathways (MACPath) in human cancers.PLoS computational biology · 2018Article
- Identification of core pathways based on attractor and crosstalk in ischemic stroke.Experimental and therapeutic medicine · 2018Article
- Investigation of coordination and order in transcription regulation of innate and adaptive immunity genes in type 1 diabetes.BMC medical genomics · 2017Article
- High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes.Oncotarget · 2017Article
- Altered Pathway Analyzer: A gene expression dataset analysis tool for identification and prioritization of differentially regulated and network rewired pathways.Scientific reports · 2017Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
One of the important challenges to post-genomic biology is relating observed phenotypic alterations to the underlying collective alterations in genes. Current inferential methods, however, invariably omit large bodies of information on the relationships between genes. We present a method that takes account of such information - expressed in terms of the topology of a correlation network - and we apply the method in the context of current procedures for gene set enrichment analysis.
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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.