ArticleBMC bioinformatics2012
graphite - a Bioconductor package to convert pathway topology to gene network.
Article in BMC bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 120 papers, 1 of them a synthesis that pooled it.
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Who cites it
120 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A signaling pathway-driven bioinformatics pipeline for predicting therapeutics against emerging infectious diseases.F1000Research · 2021Pooled it
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- Extracellular vesicle proteomics uncovers energy metabolism, complement system, and endoplasmic reticulum stress response dysregulation postexercise in males with myalgic encephalomyelitis/chronic fatigue syndrome.Clinical and translational medicine · 2025Article
- Strategies to include prior knowledge in omics analysis with deep neural networks.Patterns (New York, N.Y.) · 2025Review
- AMEND 2.0: module identification and multi-omic data integration with multiplex-heterogeneous graphs.BMC bioinformatics · 2025Article
- Improving drug repositioning with negative data labeling using large language models.Journal of cheminformatics · 2025Article
- Spectral divergence prioritizes key classes, genes, and pathways shared between substance use disorders and cardiovascular disease.Frontiers in neuroscience · 2025Article
- Target repositioning using multi-layer networks and machine learning: The case of prostate cancer.Computational and structural biotechnology journal · 2024Article
- Bioactivated Glucoraphanin Modulates Genes Involved in Necroptosis on Motor-Neuron-like Nsc-34: A Transcriptomic Study.Antioxidants (Basel, Switzerland) · 2024Article
- Unraveling epigenomic signatures and effectiveness of electroconvulsive therapy in treatment-resistant depression patients: a prospective longitudinal study.Clinical epigenetics · 2024Article
- Temperature-driven coordination of circadian transcriptional regulation.PLoS computational biology · 2024Article
60 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGene set analysis is moving towards considering pathway topology as a crucial feature. Pathway elements are complex entities such as protein complexes, gene family members and chemical compounds. The conversion of pathway topology to a gene/protein networks (where nodes are a simple element like a gene/protein) is a critical and challenging task that enables topology-based gene set analyses.Unfortunately, currently available R/Bioconductor packages provide pathway networks only from single databases. They do not propagate signals through chemical compounds and do not differentiate between complexes and gene families.
resultsHere we present graphite, a Bioconductor package addressing these issues. Pathway information from four different databases is interpreted following specific biologically-driven rules that allow the reconstruction of gene-gene networks taking into account protein complexes, gene families and sensibly removing chemical compounds from the final graphs. The resulting networks represent a uniform resource for pathway analyses. Indeed, graphite provides easy access to three recently proposed topological methods. The graphite package is available as part of the Bioconductor software suite.
conclusionsgraphite is an innovative package able to gather and make easily available the contents of the four major pathway databases. In the field of topological analysis graphite acts as a provider of biological information by reducing the pathway complexity considering the biological meaning of the pathway elements.
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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.