ArticleMolecular systems biology2021
DOMINO: a network-based active module identification algorithm with reduced rate of false calls.
Article in Molecular systems biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
46 citing papers in PubMed.
- A Framework for Benchmarking Pathway Reconstruction Algorithms.bioRxiv : the preprint server for biology · 2026Article
- A module-based approach for post-omics, post-GWAS network-based gene classification.Bioinformatics (Oxford, England) · 2026Article
- Inferring and evaluating network medicine-based disease modules with nextflow.Bioinformatics (Oxford, England) · 2026Article
- A statistical physics approach to integrating multi-omics data for disease-module detection.Cell reports methods · 2025Article
- Evaluation and Aggregation of Active Module Identification Algorithms.bioRxiv : the preprint server for biology · 2025Article
- Article
- Drug Repurposing for Kala-Azar.Pharmaceutics · 2025Article
- Charting γ-secretase substrates by explainable AI.Nature communications · 2025Article
- Inference of differential kinase interaction networks with KINference.Bioinformatics (Oxford, England) · 2025Article
- An integrative systems-biology approach defines mechanisms of Alzheimer's disease neurodegeneration.Nature communications · 2025Article
- A new Similarity Based Adapted Louvain Algorithm (SIMBA) for active module identification in p-value attributed biological networks.Scientific reports · 2025Article
- AMEND 2.0: module identification and multi-omic data integration with multiplex-heterogeneous graphs.BMC bioinformatics · 2025Article
- NetworkCommons: bridging data, knowledge, and methods to build and evaluate context-specific biological networks.Bioinformatics (Oxford, England) · 2025Article
- A collaborative network analysis for the interpretation of transcriptomics data in Huntington's disease.Scientific reports · 2025Article
- A comprehensive benchmark study of methods for identifying significantly perturbed subnetworks in cancer.Briefings in bioinformatics · 2024Article
- Maternal genetic variants in kinesin motor domains prematurely increase egg aneuploidy.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- A fundamental study on postmortem submersion interval estimation by metabolomics analyzing of gastrocnemius muscle from submersed rat models in freshwater.International journal of legal medicine · 2024Article
- Disease gene prioritization with quantum walks.Bioinformatics (Oxford, England) · 2024Article
- Unveiling hidden connections in omics data via pyPARAGON: an integrative hybrid approach for disease network construction.Briefings in bioinformatics · 2024Article
- Drugst.One - a plug-and-play solution for online systems medicine and network-based drug repurposing.Nucleic acids research · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Algorithms for active module identification (AMI) are central to analysis of omics data. Such algorithms receive a gene network and nodes' activity scores as input and report subnetworks that show significant over-representation of accrued activity signal ("active modules"), thus representing biological processes that presumably play key roles in the analyzed conditions. Here, we systematically evaluated six popular AMI methods on gene expression and GWAS data. We observed that GO terms enriched in modules detected on the real data were often also enriched on modules found on randomly permuted data. This indicated that AMI methods frequently report modules that are not specific to the biological context measured by the analyzed omics dataset. To tackle this bias, we designed a permutation-based method that empirically evaluates GO terms reported by AMI methods. We used the method to fashion five novel AMI performance criteria. Last, we developed DOMINO, a novel AMI algorithm, that outperformed the other six algorithms in extensive testing on GE and GWAS data. Software is available at https://github.com/Shamir-Lab.
Indexed as
Identifiers
What OpenQuestion holds
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.