ArticleNucleic acids research2011
COXPRESdb: a database to compare gene coexpression in seven model animals.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- Integrative spatial omics reveals distinct tumor-promoting multicellular niches and immunosuppressive mechanisms in Black American and White American patients with TNBC.Nature communications · 2025Article
- COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations.Nucleic acids research · 2023Article
- Gene expression patterns associated with caudal fin shape in the cichlidHydrobiologia · 2023Article
- Network-guided search for genetic heterogeneity between gene pairs.Bioinformatics (Oxford, England) · 2021Article
- COXPRESdb v7: a gene coexpression database for 11 animal species supported by 23 coexpression platforms for technical evaluation and evolutionary inference.Nucleic acids research · 2019Article
- Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data.Nature biotechnology · 2018Article
- Towards a gene regulatory network shaping the fins of the Princess cichlid.Scientific reports · 2018Article
- ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index.Plant & cell physiology · 2018Article
- Article
- Modular reorganization of the global network of gene regulatory interactions during perinatal human brain development.BMC developmental biology · 2016Article
- Article
- ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression.Plant & cell physiology · 2016Article
- Proportionality: a valid alternative to correlation for relative data.PLoS computational biology · 2015Article
- A systems-level approach to parental genomic imprinting: the imprinted gene network includes extracellular matrix genes and regulates cell cycle exit and differentiation.Genome research · 2015Article
- Modular and coordinated expression of immune system regulatory and signaling components in the developing and adult nervous system.Frontiers in cellular neuroscience · 2015Article
- Protein complex discovery by interaction filtering from protein interaction networks using mutual rank coexpression and sequence similarity.BioMed research international · 2015Article
- MIrExpress: A Database for Gene Coexpression Correlation in Immune Cells Based on Mutual Information and Pearson Correlation.Journal of immunology research · 2015Article
- Article
- COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems.Nucleic acids research · 2015Article
- Spotlite: web application and augmented algorithms for predicting co-complexed proteins from affinity purification--mass spectrometry data.Journal of proteome research · 2014Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Publicly available databases of coexpressed gene sets are a valuable resource for a wide variety of experimental studies, including gene targeting for functional identification, and for investigations of regulatory mechanisms or protein-protein interaction networks. Although coexpressed gene databases are becoming more and more popular in the field of plant biology, those with animal data are rather limited, possibly due to the lower reliability of the coexpression data. The original COXPRESdb (coexpressed gene database) (http://coxpresdb.jp) represented the coexpression relationship for human and mouse. Here, we report updates of this database that especially focus on the enhancement of the reliability of gene coexpression data in animals. For this purpose, we implemented a new comparable coexpression measure, Mutual Rank, included five other animal species, rat, chicken, zebrafish, fly and nematoda, to assess the conservation of coexpression, and added different layers of omics data into the integrated network of genes. Comparison of coexpression is a key concept to enhance the reliability of gene coexpression, and the integration of different information can reduce the noise inherent in the information. With the functions for gene network representation, COXPRESdb can help researchers to clarify the functional and regulatory networks of genes in a broad array of animal species.
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