ArticlePLoS computational biology2021
netgsa: Fast computation and interactive visualization for topology-based pathway enrichment analysis.
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
8 citing papers in PubMed.
- Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks.Genome research · 2025Article
- DNEA: an R package for fast and versatile data-driven network analysis of metabolomics data.BMC bioinformatics · 2024Article
- 5'-Isoforms of miR-1246 Have Distinct Targets and Stronger Functional Impact Compared with Canonical miR-1246 in Colorectal Cancer Cells In Vitro.International journal of molecular sciences · 2024Article
- KNeXT: a NetworkX-based topologically relevant KEGG parser.Frontiers in genetics · 2024Article
- Combining network pharmacology and experimental verification to reveal the mechanism of Chaigui granules in the treatment of depression through PI3K/Akt/mTOR signaling pathways.Metabolic brain disease · 2023Article
- Metabolic Pathway Analysis: Advantages and Pitfalls for the Functional Interpretation of Metabolomics and Lipidomics Data.Biomolecules · 2023Article
- PSF toolkit: an R package for pathway curation and topology-aware analysis.Frontiers in genetics · 2023Article
- SEMgsa: topology-based pathway enrichment analysis with structural equation models.BMC bioinformatics · 2022Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Existing software tools for topology-based pathway enrichment analysis are either computationally inefficient, have undesirable statistical power, or require expert knowledge to leverage the methods' capabilities. To address these limitations, we have overhauled NetGSA, an existing topology-based method, to provide a computationally-efficient user-friendly tool that offers interactive visualization. Pathway enrichment analysis for thousands of genes can be performed in minutes on a personal computer without sacrificing statistical power. The new software also removes the need for expert knowledge by directly curating gene-gene interaction information from multiple external databases. Lastly, by utilizing the capabilities of Cytoscape, the new software also offers interactive and intuitive network visualization.
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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.