ArticleNeurology. Genetics2016
In silico prioritization based on coexpression can aid epileptic encephalopathy gene discovery.
Article in Neurology. Genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 1 of them a synthesis that pooled it.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
19 citing papers in PubMed, 1 synthesis or guideline pooled it, 22 citations in OpenAlex.
- Pooled it
- Solving the Etiology of Developmental and Epileptic Encephalopathy with Spike-Wave Activation in Sleep (D/EE-SWAS).Annals of neurology · 2024Article
- Identification of SYNJ1 in a Complex Case of Juvenile Parkinsonism Using a Multiomics Approach.International journal of molecular sciences · 2024Article
- Molecular subtypes of epilepsy associated with post-surgical seizure recurrence.Brain communications · 2023Article
- PlexinA1-deficient mice exhibit decreased cell density and augmented oxidative stress in parvalbumin-expressing interneurons in the medial prefrontal cortex.IBRO neuroscience reports · 2022Article
- Genetic and molecular features of seizure-freedom following surgical resections for focal epilepsy: A pilot study.Frontiers in neurology · 2022Article
- Biallelic and monoallelic variants in PLXNA1 are implicated in a novel neurodevelopmental disorder with variable cerebral and eye anomalies.Genetics in medicine : official journal of the American College of Medical Genetics · 2021Article
- Kallmann syndrome and idiopathic hypogonadotropic hypogonadism: The role of semaphorin signaling on GnRH neurons.Handbook of clinical neurology · 2021Review
- PlexinA1 deficiency in BALB/cAJ mice leads to excessive self-grooming and reduced prepulse inhibition.IBRO reports · 2020Article
- Genome-wide profiling of long noncoding RNA expression patterns and CeRNA analysis in mouse cortical neurons infected with different strains of borna disease virus.Genes & diseases · 2019Article
- Article
- NBEA: Developmental disease gene with early generalized epilepsy phenotypes.Annals of neurology · 2018Article
- De novo and inherited private variants in MAP1B in periventricular nodular heterotopia.PLoS genetics · 2018Article
- Regulation of neuronal survival by DNA methyltransferases.Neural regeneration research · 2017Review
- De Novo Mutations in PPP3CA Cause Severe Neurodevelopmental Disease with Seizures.American journal of human genetics · 2017Article
- De Novo Mutations in YWHAG Cause Early-Onset Epilepsy.American journal of human genetics · 2017Article
- PLXNA1 developmental encephalopathy with syndromic features: A case report and review of the literature.American journal of medical genetics. Part A · 2017Article
- brain-coX: investigating and visualising gene co-expression in seven human brain transcriptomic datasets.Genome medicine · 2017Article
- Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
objectiveTo evaluate the performance of an in silico prioritization approach that was applied to 179 epileptic encephalopathy candidate genes in 2013 and to expand the application of this approach to the whole genome based on expression data from the Allen Human Brain Atlas.
methodsPubMed searches determined which of the 179 epileptic encephalopathy candidate genes had been validated. For validated genes, it was noted whether they were 1 of the 19 of 179 candidates prioritized in 2013. The in silico prioritization approach was applied genome-wide; all genes were ranked according to their coexpression strength with a reference set (i.e., 51 established epileptic encephalopathy genes) in both adult and developing human brain expression data sets. Candidate genes ranked in the top 10% for both data sets were cross-referenced with genes previously implicated in the epileptic encephalopathies due to a de novo variant.
resultsFive of 6 validated epileptic encephalopathy candidate genes were among the 19 prioritized in 2013 (odds ratio = 54, 95% confidence interval [7,∞], p = 4.5 × 10(-5), Fisher exact test); one gene was false negative. A total of 297 genes ranked in the top 10% for both the adult and developing brain data sets based on coexpression with the reference set. Of these, 9 had been previously implicated in the epileptic encephalopathies (FBXO41, PLXNA1, ACOT4, PAK6, GABBR2, YWHAG, NBEA, KNDC1, and SELRC1).
conclusionsWe conclude that brain gene coexpression data can be used to assist epileptic encephalopathy gene discovery and propose 9 genes as strong epileptic encephalopathy candidates worthy of further investigation.
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Registered trials
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.