ArticlePloS one2014
Integrated pathway clusters with coherent biological themes for target prioritisation.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Genome-wide association study of psychiatric and substance use comorbidity in Mexican individuals.Scientific reports · 2021Article
- Investigation of multiple sclerosis-related pathways through the integration of genomic and proteomic data.PeerJ · 2021Article
- From miRNA Target Gene Network to miRNA Function: miR-375 Might Regulate Apoptosis and Actin Dynamics in the Heart Muscle via Rho-GTPases-Dependent Pathways.International journal of molecular sciences · 2020Article
- A Machine Learning Approach to Predicting Autism Risk Genes: Validation of Known Genes and Discovery of New Candidates.Frontiers in genetics · 2020Article
- Potential Marker Pathways in the Endometrium That May Cause Recurrent Implantation Failure.Reproductive sciences (Thousand Oaks, Calif.) · 2019Article
- The TargetMine Data Warehouse: Enhancement and Updates.Frontiers in genetics · 2019Article
- ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases.NPJ systems biology and applications · 2019Article
- The microRNA-29/PGC1α regulatory axis is critical for metabolic control of cardiac function.PLoS biology · 2018Article
- Interactive Toxicogenomics: Gene set discovery, clustering and analysis in Toxygates.Scientific reports · 2017Article
- An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework.Database : the journal of biological databases and curation · 2016Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Prioritising candidate genes for further experimental characterisation is an essential, yet challenging task in biomedical research. One way of achieving this goal is to identify specific biological themes that are enriched within the gene set of interest to obtain insights into the biological phenomena under study. Biological pathway data have been particularly useful in identifying functional associations of genes and/or gene sets. However, biological pathway information as compiled in varied repositories often differs in scope and content, preventing a more effective and comprehensive characterisation of gene sets. Here we describe a new approach to constructing biologically coherent gene sets from pathway data in major public repositories and employing them for functional analysis of large gene sets. We first revealed significant overlaps in gene content between different pathways and then defined a clustering method based on the shared gene content and the similarity of gene overlap patterns. We established the biological relevance of the constructed pathway clusters using independent quantitative measures and we finally demonstrated the effectiveness of the constructed pathway clusters in comparative functional enrichment analysis of gene sets associated with diverse human diseases gathered from the literature. The pathway clusters and gene mappings have been integrated into the TargetMine data warehouse and are likely to provide a concise, manageable and biologically relevant means of functional analysis of gene sets and to facilitate candidate gene prioritisation.
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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.