ArticleNucleic acids research2015
COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems.
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 97 papers, 2 of them syntheses that pooled it.
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Who cites it
97 citing papers in PubMed, 2 syntheses or guidelines pooled it.
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- Benchmark of computational methods to detect digenism in sequencing data.European journal of human genetics : EJHG · 2025Review
- Prediction of lncRNA functions using deep neural networks based on multiple networks.BMC genomics · 2023Article
- COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations.Nucleic acids research · 2023Article
- BERTwalk for integrating gene networks to predict gene- to pathway-level properties.Bioinformatics advances · 2023Article
- Rational Approach to Finding Genes Encoding Molecular Biomarkers: Focus on Breast Cancer.Genes · 2022Article
- Approaches in Gene Coexpression Analysis in Eukaryotes.Biology · 2022Review
- Downregulation of CRTC1 Is Involved in CUMS-Induced Depression-Like Behavior in the Hippocampus and Its RNA Sequencing Analysis.Molecular neurobiology · 2022Article
- Degron masking outlines degronons, co-degrading functional modules in the proteome.Communications biology · 2022Article
- Tmem174, a regulator of phosphate transporter prevents hyperphosphatemia.Scientific reports · 2022Article
- Co-Expression Networks Unveiled Long Non-Coding RNAs as Molecular Targets of Drugs Used to Treat Bipolar Disorder.Frontiers in pharmacology · 2022Article
- Conditional transcriptional relationships may serve as cancer prognostic markers.BMC medical genomics · 2021Article
- Identifying digenic disease genes via machine learning in the Undiagnosed Diseases Network.American journal of human genetics · 2021Article
- Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students.Database : the journal of biological databases and curation · 2021Article
- A genome-wide atlas of co-essential modules assigns function to uncharacterized genes.Nature genetics · 2021Article
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7 authors.
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Abstract
The COXPRESdb (http://coxpresdb.jp) provides gene coexpression relationships for animal species. Here, we report the updates of the database, mainly focusing on the following two points. For the first point, we added RNAseq-based gene coexpression data for three species (human, mouse and fly), and largely increased the number of microarray experiments to nine species. The increase of the number of expression data with multiple platforms could enhance the reliability of coexpression data. For the second point, we refined the data assessment procedures, for each coexpressed gene list and for the total performance of a platform. The assessment of coexpressed gene list now uses more reasonable P-values derived from platform-specific null distribution. These developments greatly reduced pseudo-predictions for directly associated genes, thus expanding the reliability of coexpression data to design new experiments and to discuss experimental results.
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