ArticleNucleic acids research2009
SubpathwayMiner: a software package for flexible identification of pathways.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 97 papers, 2 of them syntheses that pooled it.
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Who cites it
97 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Identification of a robust functional subpathway signature for pancreatic ductal adenocarcinoma by comprehensive and integrated analyses.Cell communication and signaling : CCS · 2020Pooled it
- Conserved toxic responses across divergent phylogenetic lineages: a meta-analysis of the neurotoxic effects of RDX among multiple species using toxicogenomics.Ecotoxicology (London, England) · 2011Pooled it
- Machine learning approaches for predicting the small molecule-miRNA associations: a comprehensive review.Molecular diversity · 2025Review
- Optimizing drug combination and mechanism analysis based on risk pathway crosstalk in pan cancer.Scientific data · 2024Article
- scATAC-Ref: a reference of scATAC-seq with known cell labels in multiple species.Nucleic acids research · 2024Article
- A Subpathway and Target Gene Cluster-Based Approach Uncovers lncRNAs Associated with Human Primordial Follicle Activation.International journal of molecular sciences · 2023Article
- The Knowns and Unknowns in Protein-Metabolite Interactions.International journal of molecular sciences · 2023Review
- A novel method to identify and characterize personalized functional driver lncRNAs in cancer samples.Computational and structural biotechnology journal · 2023Article
- A comprehensive survey of the approaches for pathway analysis using multi-omics data integration.Briefings in bioinformatics · 2022Review
- CTpathway: a CrossTalk-based pathway enrichment analysis method for cancer research.Genome medicine · 2022Article
- Exploring autophagy-related prognostic genes of Alzheimer's disease based on pathway crosstalk analysis.Bosnian journal of basic medical sciences · 2022Article
- Comprehensive analysis of microglia gene and subpathway signatures for glioma prognosis and drug screening: linking microglia to glioma.Journal of translational medicine · 2022Article
- Prioritizing key synergistic circulating microRNAs for the early diagnosis of biliary tract cancer.Frontiers in oncology · 2022Article
- Prognostic Features of the Tumor Immune Microenvironment in Glioma and Their Clinical Applications: Analysis of Multiple Cohorts.Frontiers in immunology · 2022Article
- Identification of miRNA-Mediated Subpathways as Prostate Cancer Biomarkers Based on Topological Inference in a Machine Learning Process Using Integrated Gene and miRNA Expression Data.Frontiers in genetics · 2021Article
- Characterization of super-enhancer-associated functional lncRNAs acting as ceRNAs in ESCC.Molecular oncology · 2020Article
- Leucine-Rich Diet Modulates the Metabolomic and Proteomic Profile of Skeletal Muscle during Cancer Cachexia.Cancers · 2020Article
- The implementation of drug reposition for alcoholic hepatitis based on a sub-pathway integration strategy.Annals of translational medicine · 2020Article
- Comprehensive analysis of mRNA-level and miRNA-level subpathway activities for identifying robust ovarian cancer prognostic signatures.Journal of cellular and molecular medicine · 2020Article
- Article
37 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With the development of high-throughput experimental techniques such as microarray, mass spectrometry and large-scale mutagenesis, there is an increasing need to automatically annotate gene sets and identify the involved pathways. Although many pathway analysis tools are developed, new tools are still needed to meet the requirements for flexible or advanced analysis purpose. Here, we developed an R-based software package (SubpathwayMiner) for flexible pathway identification. SubpathwayMiner facilitates sub-pathway identification of metabolic pathways by using pathway structure information. Additionally, SubpathwayMiner also provides more flexibility in annotating gene sets and identifying the involved pathways (entire pathways and sub-pathways): (i) SubpathwayMiner is able to provide the most up-to-date pathway analysis results for users; (ii) SubpathwayMiner supports multiple species ( approximately 100 eukaryotes, 714 bacteria and 52 Archaea) and different gene identifiers (Entrez Gene IDs, NCBI-gi IDs, UniProt IDs, PDB IDs, etc.) in the KEGG GENE database; (iii) the system is quite efficient in cooperating with other R-based tools in biology. SubpathwayMiner is freely available at http://cran.r-project.org/web/packages/SubpathwayMiner/.
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Registered trials
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