ArticleNucleic acids research2006
Topology-based cancer classification and related pathway mining using microarray data.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed.
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- Targeted metabolomic profiling of low and high grade serous epithelial ovarian cancer tissues: a pilot study.Metabolomics : Official journal of the Metabolomic Society · 2018Article
- MultiDCoX: Multi-factor analysis of differential co-expression.BMC bioinformatics · 2017Article
- Investigation of coordination and order in transcription regulation of innate and adaptive immunity genes in type 1 diabetes.BMC medical genomics · 2017Article
- Integration of gene expression and DNA-methylation profiles improves molecular subtype classification in acute myeloid leukemia.BMC bioinformatics · 2015Article
- Predicting disease-related subnetworks for type 1 diabetes using a new network activity score.Omics : a journal of integrative biology · 2012Article
- Finding minimum gene subsets with heuristic breadth-first search algorithm for robust tumor classification.BMC bioinformatics · 2012Article
- Pathway-based identification of a smoking associated 6-gene signature predictive of lung cancer risk and survival.Artificial intelligence in medicine · 2012Article
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- LRRN4 and UPK3B are markers of primary mesothelial cells.PloS one · 2011Article
- A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis.Bioinformatics (Oxford, England) · 2009Article
- Topological and organizational properties of the products of house-keeping and tissue-specific genes in protein-protein interaction networks.BMC systems biology · 2009Article
- An integrated method for cancer classification and rule extraction from microarray data.Journal of biomedical science · 2009Article
- Differential dependency network analysis to identify condition-specific topological changes in biological networks.Bioinformatics (Oxford, England) · 2009Article
- An integrative approach to characterize disease-specific pathways and their coordination: a case study in cancer.BMC genomics · 2008Article
- TAPPA: topological analysis of pathway phenotype association.Bioinformatics (Oxford, England) · 2007Article
- Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis.BMC bioinformatics · 2007Article
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8 authors.
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Abstract
Cancer classification is the critical basis for patient-tailored therapy, while pathway analysis is a promising method to discover the underlying molecular mechanisms related to cancer development by using microarray data. However, linking the molecular classification and pathway analysis with gene network approach has not been discussed yet. In this study, we developed a novel framework based on cancer class-specific gene networks for classification and pathway analysis. This framework involves a novel gene network construction, named ordering network, which exhibits the power-law node-degree distribution as seen in correlation networks. The results obtained from five public cancer datasets showed that the gene networks with ordering relationship are better than those with correlation relationship in terms of accuracy and stability of the classification performance. Furthermore, we integrated the ordering networks, classification information and pathway database to develop the topology-based pathway analysis for identifying cancer class-specific pathways, which might be essential in the biological significance of cancer. Our results suggest that the topology-based classification technology can precisely distinguish cancer subclasses and the topology-based pathway analysis can characterize the correspondent biochemical pathways even if there are subtle, but consistent, changes in gene expression, which may provide new insights into the underlying molecular mechanisms of tumorigenesis.
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