ArticleNature protocols2016
Analyzing and interpreting genome data at the network level with ConsensusPathDB.
Article in Nature protocols, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 271 papers, 5 of them syntheses that pooled it.
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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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
271 citing papers in PubMed, 5 syntheses or guidelines pooled it.
- Gene expression signatures of response to fluoxetine treatment: systematic review and meta-analyses.Molecular psychiatry · 2025Pooled it
- Graph databases in systems biology: a systematic review.Briefings in bioinformatics · 2024Pooled it
- Interactions between genes altered during cardiotoxicity and neurotoxicity in zebrafish revealed using induced network modules analysis.Scientific reports · 2023Pooled it
- Multi-ancestry genome-wide association analyses improve resolution of genes and pathways influencing lung function and chronic obstructive pulmonary disease risk.Nature genetics · 2023Pooled it
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- Synergistic cooperation between progranulin and Jak2/Stat3 signaling determines definitive myeloid cell fate.Cell reports · 2026Article
- Integrative metabolite-protein interaction networks reveal potential pathways and biomarkers in sepsis.BMC infectious diseases · 2026Article
- Network resilience of the human interactome to pan-cancer mutations reveals conserved pathway vulnerabilities.iScience · 2026Article
- Proteome profiles of esophageal squamous cell carcinoma tie mitochondrial complex I to immunotherapy.EMBO molecular medicine · 2026Article
- Multiplex networks-based directed graph neural network for cancer driver gene identification.PLoS computational biology · 2026Article
- LINE-1 Locus Transcription Nucleates Oncogenic Chromatin Architecture.Cancer discovery · 2026Article
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211 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
ConsensusPathDB consists of a comprehensive collection of human (as well as mouse and yeast) molecular interaction data integrated from 32 different public repositories and a web interface featuring a set of computational methods and visualization tools to explore these data. This protocol describes the use of ConsensusPathDB (http://consensuspathdb.org) with respect to the functional and network-based characterization of biomolecules (genes, proteins and metabolites) that are submitted to the system either as a priority list or together with associated experimental data such as RNA-seq. The tool reports interaction network modules, biochemical pathways and functional information that are significantly enriched by the user's input, applying computational methods for statistical over-representation, enrichment and graph analysis. The results of this protocol can be observed within a few minutes, even with genome-wide data. The resulting network associations can be used to interpret high-throughput data mechanistically, to characterize and prioritize biomarkers, to integrate different omics levels, to design follow-up functional assay experiments and to generate topology for kinetic models at different scales.
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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.