NeuroPsychiatric Mutation Knowledge Base

About

Welcome to our open access database PsyMuKB.


PsyMuKB is a comprehensive knowledge base that links transcriptional and translational annotations to de novo variants, which are found in subjects but not in their parents, in developmental and neuropsychiatric disorders. Large-scale genomic and proteomic data are integrated into PsyMuKB, including developmental brain expressions, neuronal single-cell transcriptome, regulatory elements, and transcript annotations, protein-protein interactions (PPI) and protein isoform expressions. It aims to provide users with a comprehensive data exploration of de novo variants, such as their genomic locations on alternatively spliced isoforms, expression patterns of the mutation-disrupted genes and/or isoforms, and interaction network of impacted proteins.


We provide detailed annotations for various types of de novo variants, such as single nucleotide variations (SNVs), small insertions and deletions (indels) and copy number variations (CNVs). It currently contains >876,178 curated de novo variants, including coding and non-coding (~15,852 cases and ~7,802 controls) from more than 123 published studies of >25 neural and developmental diseases, including Autism Spectrum Disorder (ASD), Bipolar Disorder (BD), Developmental Delay (DD), Intellectual Disability (ID), Obsessive Compulsive Disorder (OCD), Schizophrenia (SCZ), Tourette Disorder (TD), Alzheimer early-onset (AD), etc., and unaffected siblings as control (CTR). (Detail in Document)


PsyMuKB will be updated regularly to provide the research community with an up-to-date knowledge base. When using PsyMuKB, please feel free to start with the Document section. Publication detail：PsyMuKB: An Integrative De Novo Variant Knowledge Base for Developmental Disorders.

Quick search


• Gene symbol e.g. SHANK3
• Gene ID e.g. 9527
• Chr. position e.g. chr11:11186630-12284618

Variants with brain expression





We compile different sets of tissues and neuronal cell-specific brain expression data, including spatio-temporal human brain developmental expression data from BrainSpan, human brain isoform expression data from GTEx, and single-cell human (Zhong et. al. 2018) & mouse RNA-seq brain expression data (Saunders et. al. 2018). The brain expression patterns are mapped to genes and can be visualized for in-depth mutation explorations.

Variant visualizations


We curate a comprehensive list of >876,178 de novo variants from >25 neuropsychiatric disorders with functional annotations, and map them to all the alternatively spliced isoforms and regulatory elements, such as promoters and enhancers, of the impacted gene. Meanwhile, >800 de novo CNVs are aligned by gene location in chromatins. All information can be exported in various formats.

Explore DNMs at isoform-level


Interface design is executed to study focused mutations like coding DNM, non-coding DNM, and CNVs. To a certain variant, independent information is showed according to its mRNA and protein expression levels. Personal choices are accepted to present special expression patterns.

Interactome and structure





We provide >409,000 curated experimentally-determined high-quality human physical protein-protein interactions (PPI) from BioGRID v3.5.165 Interactome Resource. Interactions are filtered both systematically and manually to remove low-quality interactions. The node of Interactome Networks showing on our website is limited under 200 to properly organization. PPIs can be exported in various formats.

Data statistics
Data type Source Count
De novo variants from psychiatric disorder studies De novo mutation (DNM) 876,178 mutations
Copy number variation (CNV) 841 CNVs
Gene expressions Spatio-temporal brain expression (BrainSpan) 15,383 genes
Single cell RNA-seq of mouse brain 22,460 genes
Single cell RNA-seq of human brain 22,087 genes
Various tissues expression of the human body (GTEx v7) 56,200 genes
mRNA transcripts expression GTEx v7 196,520 transcripts
Protein (including isoforms) expression ProteomicsDB v2018.09 18,634 genes (43,015 isoforms)
Regulatory elements Promoter (FANTOM5) 82,149 promoters
Enhancer (Genehancer) 250,733 enhancers
Transcript annotations Refseq v2017.09 58,384 transcripts
Gencode v19 196,520 transcripts
Protein-protein interaction (PPI) BioGRID v3.5 409,173 pairs
Distribution of disease variants