Table 1.

Summary of features in ASPIREdb.

Feature	Description
Security
Access control list	Data access is restricted to project owners, administrators and collaborators. Projects can be shared between users of the same user group.
Visualization
Label Manager	Labels help identify subjects or variants of interest visually. Labels can also be used as a filter criteria.
Ideogram viewer	Quickly get an overview of where in the genome the variants are located. Variants can be colored by type and label.
Phenotype heatmap	Subjects and phenotype values are displayed in a heatmap with automatic clustering along rows and columns.
Interactive user interface	Interactive highlighting of subject, variants and phenotypes.
Analysis
Query interface	Build simple queries such as filtering variants by location to more complex queries that involve both location and get set overlap.
Burden Analysis	Group patients by subject labels and compare differences between subject groups. For example, do patients in one group tend to have more variants that affect genes? Is a group more enriched for a certain phenotype?
Gene set manager	Upload set of genes of interest and identify which variants are located in these genes.
Compound heterozygote detection	Identify which variants are in the same gene of each patient.
Phenotype contingency table	Quickly stratify subjects based on a subset of phenotypes.
Gene annotation	Ensembl genes are automatically assigned to variants.
Integration
Human Phenotype Ontology integration	Lookup HPO IDs and display the corresponding HPO terms. Parent and child HPO terms are resolved during a Phenotype filter.
Gemma integration	Look for genes that are coexpressed with the genes hit by a variant.
Phenocarta integration	Display genes associated with an HPO phenotype.
UCSC Genome Browser integration	View variants as UCSC tracks and highlight genomic features such as sequence conservation, regulatory regions and expression levels.
DECIPHER and DGV Overlap	Identify which variants are found in patients (DECIPHER) and controls (DGV).
Reports
Variant Report	Display the frequency of variants for the selected variant characteristic as a table or barchart format. Variant lengths are displayed as a histogram which can be Log2 transformed. Barcharts are grouped by Subject Labels.