ArticleBioinformatics (Oxford, England)2014
NetPathMiner: R/Bioconductor package for network path mining through gene expression.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Predicting GD2 expression across cancer types by the integration of pathway topology and transcriptome data.Frontiers in bioinformatics · 2025Article
- Unraveling the glycosphingolipid metabolism by leveraging transcriptome-weighted network analysis on neuroblastic tumors.Cancer & metabolism · 2024Article
- COPS: A novel platform for multi-omic disease subtype discovery via robust multi-objective evaluation of clustering algorithms.PLoS computational biology · 2024Article
- Robustness evaluations of pathway activity inference methods on gene expression data.BMC bioinformatics · 2024Article
- Article
- CTpathway: a CrossTalk-based pathway enrichment analysis method for cancer research.Genome medicine · 2022Article
- Analysing the meta-interaction between pathways by gene set topological impact analysis.BMC genomics · 2020Article
- GeneSetCluster: a tool for summarizing and integrating gene-set analysis results.BMC bioinformatics · 2020Article
- Concurrent lipidomics and proteomics on malignant plasma cells from multiple myeloma patients: Probing the lipid metabolome.PloS one · 2020Article
- Comparative transcriptomics with self-organizing map reveals cryptic photosynthetic differences between two accessions of North American Lake cress.Scientific reports · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
unlabelledNetPathMiner is a general framework for mining, from genome-scale networks, paths that are related to specific experimental conditions. NetPathMiner interfaces with various input formats including KGML, SBML and BioPAX files and allows for manipulation of networks in three different forms: metabolic, reaction and gene representations. NetPathMiner ranks the obtained paths and applies Markov model-based clustering and classification methods to the ranked paths for easy interpretation. NetPathMiner also provides static and interactive visualizations of networks and paths to aid manual investigation. AVAILABILITY: The package is available through Bioconductor and from Github at http://github.com/ahmohamed/NetPathMiner.
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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.