ArticleBMC bioinformatics2009
Identification of differentially expressed subnetworks based on multivariate ANOVA.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 32 citations in OpenAlex.
- Smell Detection Agent Optimisation Framework and Systems Biology Approach to Detect Dys-Regulated Subnetwork in Cancer Data.Biomolecules · 2021Article
- Prior knowledge guided active modules identification: an integrated multi-objective approach.BMC systems biology · 2017Article
- CytoGTA: A cytoscape plugin for identifying discriminative subnetwork markers using a game theoretic approach.PloS one · 2017Article
- DIFFERENTIAL PATHWAY DEPENDENCY DISCOVERY ASSOCIATED WITH DRUG RESPONSE ACROSS CANCER CELL LINES.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2017Article
- GSNFS: Gene subnetwork biomarker identification of lung cancer expression data.BMC medical genomics · 2016Article
- KNOWLEDGE-ASSISTED APPROACH TO IDENTIFY PATHWAYS WITH DIFFERENTIAL DEPENDENCIES.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2016Article
- ChiNet uncovers rewired transcription subnetworks in tolerant yeast for advanced biofuels conversion.Nucleic acids research · 2015Article
- Pathway mapping and development of disease-specific biomarkers: protein-based network biomarkers.Journal of cellular and molecular medicine · 2015Review
- EDDY: a novel statistical gene set test method to detect differential genetic dependencies.Nucleic acids research · 2014Article
- Identification of phenotype deterministic genes using systemic analysis of transcriptional response.Scientific reports · 2014Article
- Causal inference of gene regulation with subnetwork assembly from genetical genomics data.Nucleic acids research · 2014Article
- Integrative approaches for finding modular structure in biological networks.Nature reviews. Genetics · 2013Review
- Large Scale Chemical Cross-linking Mass Spectrometry Perspectives.Journal of proteomics & bioinformatics · 2013Article
- Article
- State of the art in silico tools for the study of signaling pathways in cancer.International journal of molecular sciences · 2012Review
- Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis.BMC systems biology · 2010Article
- Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging.Genome biology · 2010Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSince high-throughput protein-protein interaction (PPI) data has recently become available for humans, there has been a growing interest in combining PPI data with other genome-wide data. In particular, the identification of phenotype-related PPI subnetworks using gene expression data has been of great concern. Successful integration for the identification of significant subnetworks requires the use of a search algorithm with a proper scoring method. Here we propose a multivariate analysis of variance (MANOVA)-based scoring method with a greedy search for identifying differentially expressed PPI subnetworks.
resultsGiven the MANOVA-based scoring method, we performed a greedy search to identify the subnetworks with the maximum scores in the PPI network. Our approach was successfully applied to human microarray datasets. Each identified subnetwork was annotated with the Gene Ontology (GO) term, resulting in the phenotype-related functional pathway or complex. We also compared these results with those of other scoring methods such as t statistic- and mutual information-based scoring methods. The MANOVA-based method produced subnetworks with a larger number of proteins than the other methods. Furthermore, the subnetworks identified by the MANOVA-based method tended to consist of highly correlated proteins.
conclusionThis article proposes a MANOVA-based scoring method to combine PPI data with expression data using a greedy search. This method is recommended for the highly sensitive detection of large subnetworks.
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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.