ArticleBioinformatics (Oxford, England)2011
COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
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- Limitation of permutation-based differential correlation analysis.Genetic epidemiology · 2023Article
- A network embedding approach to identify active modules in biological interaction networks.Life science alliance · 2023Article
- USNAP: fast unique dense region detection and its application to lung cancer.Bioinformatics (Oxford, England) · 2023Article
- MATTE: a pipeline of transcriptome module alignment for anti-noise phenotype-gene-related analysis.Briefings in bioinformatics · 2023Article
- SEMtree: tree-based structure learning methods with structural equation models.Bioinformatics (Oxford, England) · 2023Article
- Lipid network and moiety analysis for revealing enzymatic dysregulation and mechanistic alterations from lipidomics data.Briefings in bioinformatics · 2023Article
- Facioscapulohumeral dystrophy weakened sarcomeric contractility is mimicked in induced pluripotent stem cells-derived innervated muscle fibres.Journal of cachexia, sarcopenia and muscle · 2022Article
- Temporal and sequential order of nonoverlapping gene networks unraveled in mated female Drosophila.Life science alliance · 2022Article
- Prospects and challenges of cancer systems medicine: from genes to disease networks.Briefings in bioinformatics · 2022Review
- A multi-objective genetic algorithm to find active modules in multiplex biological networks.PLoS computational biology · 2021Article
- Predicting Protein Functions Based on Differential Co-expression and Neighborhood Analysis.Journal of computational biology : a journal of computational molecular cell biology · 2021Article
- Differential Co-Expression Analyses Allow the Identification of Critical Signalling Pathways Altered during Tumour Transformation and Progression.International journal of molecular sciences · 2020Review
- Sex biased expression and co-expression networks in development, using the hymenopteran Nasonia vitripennis.PLoS genetics · 2020Article
- Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer.Genome biology · 2019Article
- GeneSurrounder: network-based identification of disease genes in expression data.BMC bioinformatics · 2019Article
- A Multi-Cohort and Multi-Omics Meta-Analysis Framework to Identify Network-Based Gene Signatures.Frontiers in genetics · 2019Article
- pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks.Frontiers in genetics · 2019Article
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4 authors.
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Abstract
motivationThe identification of condition specific sub-networks from gene expression profiles has important biological applications, ranging from the selection of disease-related biomarkers to the discovery of pathway alterations across different phenotypes. Although many methods exist for extracting these sub-networks, very few existing approaches simultaneously consider both the differential expression of individual genes and the differential correlation of gene pairs, losing potentially valuable information in the data.
resultsIn this article, we propose a new method, COSINE (COndition SpecIfic sub-NEtwork), which employs a scoring function that jointly measures the condition-specific changes of both 'nodes' (individual genes) and 'edges' (gene-gene co-expression). It uses the genetic algorithm to search for the single optimal sub-network which maximizes the scoring function. We applied COSINE to both simulated datasets with various differential expression patterns, and three real datasets, one prostate cancer dataset, a second one from the across-tissue comparison of morbidly obese patients and the other from the across-population comparison of the HapMap samples. Compared with previous methods, COSINE is more powerful in identifying truly significant sub-networks of appropriate size and meaningful biological relevance. AVAILABILITY: The R code is available as the COSINE package on CRAN: http://cran.r-project.org/web/packages/COSINE/index.html.
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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.