ArticleNucleic acids research2023
COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- CoxFormer enables spatial omics inference with multimodal generative modeling.Nature communications · 2026Article
- Constructing gene co-functional and co-regulatory networks from public transcriptomes using condition-specific ensemble co-expression.Nature communications · 2026Article
- The IGVF catalog-from genetic variation to function.Nucleic acids research · 2026Article
- Subgroup of meningiomas involving FOS and FOSB gene fusions.Nature communications · 2025Article
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- Exome analysis links kidney malformations to developmental disorders and reveals causal genes.Nature communications · 2025Article
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- Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions.Molecular cell · 2025Article
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- Microglia contribute to the production of the amyloidogenic ABri peptide in familial British dementia.Acta neuropathologica · 2024Article
- A best-match approach for gene set analyses in embedding spaces.Genome research · 2024Article
- Predictomes: A classifier-curated database of AlphaFold-modeled protein-protein interactions.bioRxiv : the preprint server for biology · 2024Article
- The Immunometabolic Gene N-Acetylglucosamine Kinase Is Uniquely Involved in the Heritability of Multiple Sclerosis Severity.International journal of molecular sciences · 2024Article
- Gene set correlation enrichment analysis for interpreting and annotating gene expression profiles.Nucleic acids research · 2024Article
- CoGTEx: Unscaled system-level coexpression estimation from GTEx data forecast novel functional gene partners.PloS one · 2024Article
- Article
- The mNature communications · 2023Article
- Article
- Multi-omics computational analysis unveils the involvement of AP-1 and CTCF in hysteresis of chromatin states during macrophage polarization.Frontiers in immunology · 2023Article
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Authors and funding
5 authors.
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Abstract
Gene coexpression is synchronization of gene expression across many cellular and environmental conditions and is widely used to infer the biological function of genes. Gene coexpression information is complex, comprising a complete graph of all genes in the genome, and requires appropriate visualization and analysis tools. Since its initial release in 2007, the animal gene expression database COXPRESdb (https://coxpresdb.jp) has been continuously improved by adding new gene coexpression data and analysis tools. Here, we report COXPRESdb version 8, which has been enhanced with new features for an overview, summary, and individual examination of coexpression relationships: CoexMap to display coexpression on a genome scale, pathway enrichment analysis to summarize the function of coexpressed genes, and CoexPub to bridges coexpression and existing knowledge. COXPRESdb also facilitates downstream analyses such as interspecies comparisons by integrating RNAseq and microarray coexpression data in a union-type gene coexpression. COXPRESdb strongly support users with the new coexpression data and enhanced functionality.
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