ArticleNucleic acids research2020
CoCoCoNet: conserved and comparative co-expression across a diverse set of species.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers, 1 of them a synthesis that pooled it.
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Who cites it
27 citing papers in PubMed, 1 synthesis or guideline pooled it, 50 citations in OpenAlex.
- Meta-analysis of single-cell RNA sequencing co-expression in human neural organoids reveals their high variability in recapitulating primary tissue.PLoS biology · 2024Pooled it
- Cell type-agnostic transcriptomic signatures enable uniform comparisons of neural maturation.PLoS biology · 2026Article
- Modular inflammation network discovery from large-scale phenotypic screening in genetically heterogeneous mouse brains.Journal of neuroinflammation · 2025Article
- Utilizing rat kidney gene co-expression networks to enhance safety assessment biomarker identification and human translation.iScience · 2025Article
- Identifying reproducible transcription regulator coexpression patterns with single cell transcriptomics.PLoS computational biology · 2025Article
- ACT2.6: Global Gene Coexpression Network inGenes · 2025Article
- Computational strategies for cross-species knowledge transfer and translational biomedicine.ArXiv · 2024Article
- Convergent evolution of plant prickles by repeated gene co-option over deep time.Science (New York, N.Y.) · 2024Article
- Massively integrated coexpression analysis reveals transcriptional regulation, evolution and cellular implications of the yeast noncanonical translatome.Genome biology · 2024Article
- Coexpression enhances cross-species integration of single-cell RNA sequencing across diverse plant species.Nature plants · 2024Article
- Defining Transcriptomic Heterogeneity between Left and Right Ventricle-Derived Cardiac Fibroblasts.Cells · 2024Article
- Comparative single-cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution.Nature ecology & evolution · 2023Article
- Preservation of co-expression defines the primary tissue fidelity of human neural organoids.bioRxiv : the preprint server for biology · 2023Article
- GeneFriends: gene co-expression databases and tools for humans and model organisms.Nucleic acids research · 2023Article
- Prevalent and dynamic binding of the cell cycle checkpoint kinase Rad53 to gene promoters.eLife · 2022Article
- Defining the extent of gene function using ROC curvature.Bioinformatics (Oxford, England) · 2022Article
- Gene co-expression analyses of health(span) across multiple species.NAR genomics and bioinformatics · 2022Article
- A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships.Genome biology · 2022Article
- Multi-Omics Approaches and Resources for Systems-Level Gene Function Prediction in the Plant Kingdom.Plants (Basel, Switzerland) · 2022Review
- In search of a Drosophila core cellular network with single-cell transcriptome data.G3 (Bethesda, Md.) · 2022Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Co-expression analysis has provided insight into gene function in organisms from Arabidopsis to zebrafish. Comparison across species has the potential to enrich these results, for example by prioritizing among candidate human disease genes based on their network properties or by finding alternative model systems where their co-expression is conserved. Here, we present CoCoCoNet as a tool for identifying conserved gene modules and comparing co-expression networks. CoCoCoNet is a resource for both data and methods, providing gold standard networks and sophisticated tools for on-the-fly comparative analyses across 14 species. We show how CoCoCoNet can be used in two use cases. In the first, we demonstrate deep conservation of a nucleolus gene module across very divergent organisms, and in the second, we show how the heterogeneity of autism mechanisms in humans can be broken down by functional groups and translated to model organisms. CoCoCoNet is free to use and available to all at https://milton.cshl.edu/CoCoCoNet, with data and R scripts available at ftp://milton.cshl.edu/data.
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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.