ArticleGenome medicine2017
brain-coX: investigating and visualising gene co-expression in seven human brain transcriptomic datasets.
Article in Genome medicine, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers, 1 of them a synthesis that pooled it.
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Who cites it
9 citing papers in PubMed, 1 synthesis or guideline pooled it.
- GWAS meta-analysis of over 29,000 people with epilepsy identifies 26 risk loci and subtype-specific genetic architecture.Nature genetics · 2023Pooled it
- Identification of potential crucial genes and therapeutic targets for epilepsy.European journal of medical research · 2024Article
- Comprehensive analyses identify potential biomarkers for encephalitis in HIV infection.Scientific reports · 2023Article
- Copy number variant analysis for syndromic congenital heart disease in the Chinese population.Human genomics · 2022Article
- NeuroSCORE is a genome-wide omics-based model that identifies candidate disease genes of the central nervous system.Scientific reports · 2022Article
- Genome-wide mega-analysis identifies 16 loci and highlights diverse biological mechanisms in the common epilepsies.Nature communications · 2018Article
- De novo and inherited private variants in MAP1B in periventricular nodular heterotopia.PLoS genetics · 2018Article
- De Novo Mutations in PPP3CA Cause Severe Neurodevelopmental Disease with Seizures.American journal of human genetics · 2017Article
- Genomic technologies-from tools to therapies.Genome medicine · 2017Article
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundThe pathogenesis of neurological and mental health disorders often involves multiple genes, complex interactions, as well as brain- and development-specific biological mechanisms. These characteristics make identification of disease genes for such disorders challenging, as conventional prioritisation tools are not specifically tailored to deal with the complexity of the human brain. Thus, we developed a novel web-application-brain-coX-that offers gene prioritisation with accompanying visualisations based on seven gene expression datasets in the post-mortem human brain, the largest such resource ever assembled.
resultsWe tested whether our tool can correctly prioritise known genes from 37 brain-specific KEGG pathways and 17 psychiatric conditions. We achieved average sensitivity of nearly 50%, at the same time reaching a specificity of approximately 75%. We also compared brain-coX's performance to that of its main competitors, Endeavour and ToppGene, focusing on the ability to discover novel associations. Using a subset of the curated SFARI autism gene collection we show that brain-coX's prioritisations are most similar to SFARI's own curated gene classifications.
conclusionsbrain-coX is the first prioritisation and visualisation web-tool targeted to the human brain and can be freely accessed via http://shiny.bioinf.wehi.edu.au/freytag.s/ .
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