ArticleNucleic acids research2013
COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
- LncRNAs SOX2-OT and NEAT1 act as a potential biomarker for esophageal squamous cell carcinoma.Discover oncology · 2024Article
- COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations.Nucleic acids research · 2023Article
- iDMET: network-based approach for integrating differential analysis of cancer metabolomics.BMC bioinformatics · 2022Article
- Association of genetic variants inFrontiers in genetics · 2022Article
- Circulating Long Non-Coding RNAs LINC00324 and LOC100507053 as Potential Liquid Biopsy Markers for Esophageal Squamous Cell Carcinoma: A Pilot Study.Frontiers in oncology · 2022Article
- TopoFun: a machine learning method to improve the functional similarity of gene co-expression modules.NAR genomics and bioinformatics · 2021Article
- TeaCoN: a database of gene co-expression network for tea plant (Camellia sinensis).BMC genomics · 2020Article
- Article
- Differential Expression of Mitochondrial Biogenesis Markers in Mouse and Human SHH-Subtype Medulloblastoma.Cells · 2019Article
- 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
- Matataki: an ultrafast mRNA quantification method for large-scale reanalysis of RNA-Seq data.BMC bioinformatics · 2018Article
- Comparative Analysis of Human Genes Frequently and Occasionally Regulated by mGenomics, proteomics & bioinformatics · 2018Article
- The Association Between AURKA Gene rs2273535 Polymorphism and Gastric Cancer Risk in a Chinese Population.Frontiers in physiology · 2018Article
- GENIUS: web server to predict local gene networks and key genes for biological functions.Bioinformatics (Oxford, England) · 2017Article
- Hsp90-downregulation influences the heat-shock response, innate immune response and onset of oocyte development in nematodes.PloS one · 2017Article
- Gene expression changes in damaged osteoarthritic cartilage identify a signature of non-chondrogenic and mechanical responses.Osteoarthritis and cartilage · 2016Article
- Systems-level analysis of human aging genes shed new light on mechanisms of aging.Human molecular genetics · 2016Article
- Exploiting single-cell expression to characterize co-expression replicability.Genome biology · 2016Article
- WeGET: predicting new genes for molecular systems by weighted co-expression.Nucleic acids research · 2016Article
- Establishing an analytic pipeline for genome-wide DNA methylation.Clinical epigenetics · 2016Review
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Coexpressed gene databases are valuable resources for identifying new gene functions or functional modules in metabolic pathways and signaling pathways. Although coexpressed gene databases are a fundamental platform in the field of plant biology, their use in animal studies is relatively limited. The COXPRESdb (http://coxpresdb.jp) provides coexpression relationships for multiple animal species, as comparisons of coexpressed gene lists can enhance the reliability of gene coexpression determinations. Here, we report the updates of the database, mainly focusing on the following two points. First, we updated our coexpression data by including recent microarray data for the previous seven species (human, mouse, rat, chicken, fly, zebrafish and nematode) and adding four new species (monkey, dog, budding yeast and fission yeast), along with a new human microarray platform. A reliability scoring function was also implemented, based on coexpression conservation to filter out coexpression with low reliability. Second, the network drawing function was updated, to implement automatic cluster analyses with enrichment analyses in Gene Ontology and in cis elements, along with interactive network analyses with Cytoscape Web. With these updates, COXPRESdb will become a more powerful tool for analyses of functional and regulatory networks of genes in a variety of animal species.
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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.