ArticleNucleic acids research2015
cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Bone marrow microenvironments that contribute to patient outcomes in newly diagnosed multiple myeloma: A cohort study of patients in the Total Therapy clinical trials.PLoS medicine · 2020Trial
- Global Stress Responses Identify the Functionally Divergent Regulators Required forExploration (Beijing, China) · 2025Article
- Predicting fitness inFrontiers in tuberculosis · 2025Article
- Context-dependent effects of CDKN2A and other 9p21 gene losses during the evolution of esophageal cancer.Nature cancer · 2025Article
- Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data.Bioinformatics (Oxford, England) · 2023Article
- MtrA modulates Mycobacterium tuberculosis cell division in host microenvironments to mediate intrinsic resistance and drug tolerance.Cell reports · 2023Article
- GRAND: a database of gene regulatory network models across human conditions.Nucleic acids research · 2022Article
- Article
- Predictive regulatory and metabolic network models for systems analysis of Clostridioides difficile.Cell host & microbe · 2021Article
- A systems-level gene regulatory network model for Plasmodium falciparum.Nucleic acids research · 2021Article
- Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium salinarum.mSystems · 2020Article
- Article
- It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data.Briefings in bioinformatics · 2019Review
- Gene co-expression analysis for functional classification and gene-disease predictions.Briefings in bioinformatics · 2018Article
- The Immune Landscape of Cancer.Immunity · 2018Article
- Transcriptional regulatory networks underlying gene expression changes in Huntington's disease.Molecular systems biology · 2018Article
- Enhancing gene regulatory network inference through data integration with markov random fields.Scientific reports · 2017Article
- An indicator cell assay for blood-based diagnostics.PloS one · 2017Article
- MiR-155-regulated molecular network orchestrates cell fate in the innate and adaptive immune response to Mycobacterium tuberculosis.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis.Cell systems · 2016Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The cMonkey integrated biclustering algorithm identifies conditionally co-regulated modules of genes (biclusters). cMonkey integrates various orthogonal pieces of information which support evidence of gene co-regulation, and optimizes biclusters to be supported simultaneously by one or more of these prior constraints. The algorithm served as the cornerstone for constructing the first global, predictive Environmental Gene Regulatory Influence Network (EGRIN) model for a free-living cell, and has now been applied to many more organisms. However, due to its computational inefficiencies, long run-time and complexity of various input data types, cMonkey was not readily usable by the wider community. To address these primary concerns, we have significantly updated the cMonkey algorithm and refactored its implementation, improving its usability and extendibility. These improvements provide a fully functioning and user-friendly platform for building co-regulated gene modules and the tools necessary for their exploration and interpretation. We show, via three separate analyses of data for E. coli, M. tuberculosis and H. sapiens, that the updated algorithm and inclusion of novel scoring functions for new data types (e.g. ChIP-seq and transcription factor over-expression [TFOE]) improve discovery of biologically informative co-regulated modules. The complete cMonkey2 software package, including source code, is available at https://github.com/baliga-lab/cmonkey2.
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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.