XGR software for enhanced interpretation of genomic summary data, illustrated by application to immunological traits

Table 1 A summary of XGR characteristics for tasks achieved and runtime required

Functions	Tasks achieved	Runtime^a
Enrichment analysis
xEnricher	A template for enrichment analysis	~40
xEnricherGenes	Gene-based enrichment analysis using a wide variety of ontologies^b	~40
xEnricherSNPs	SNP-based enrichment analysis using Experimental Factor Ontology on GWAS traits	~70
xEnricherYours	Custom-based enrichment analysis using user-defined ontologies	~5
xEnrichConciser	Removing redundant ones from enrichment outputs	~15
xEnrichBarplot	Barplot of enrichment outputs	<1
xEnrichCompare	Side-by-side barplots of comparative enrichment outputs	<1
xEnrichDAGplot	DAG plot of enrichment outputs	<1
xEnrichDAGplotAdv	DAG plot of comparative enrichment outputs	<1
Annotation analysis
xGRviaGeneAnno	Annotation analysis using nearby gene annotations by a wide variety of ontologies^b	~60
xGRviaGenomicAnno	Annotation analysis using a wide variety of genomic annotations^c	~30
Similarity analysis
xSocialiser	A template for similarity analysis	~60
xSocialiserGenes	Gene-based similarity analysis using structured ontologies on functions, diseases, and phenotypes	~70
xSocialiserSNPs	SNP-based similarity analysis using Experimental Factor Ontology on GWAS traits	~60
xCircos	Circos plot of similarity outputs	~10
xSocialiserDAGplot	DAG plot of one set of terms used for similarity analysis	<1
xSocialiserDAGplotAdv	DAG plot of two sets of terms used for similarity analysis	<1
Network analysis
xSubneterGenes	Gene-based network analysis	~60
xSubneterSNPs	SNP-based network analysis	~60
xVisNet	Network visualisation	<1

^aRuntime (measured by seconds) tested using one core on Mac OS X
^bIncluding structured ontologies on functions, diseases, and phenotypes, and non-structured ontologies on pathways, regulatory/expression signatures, druggability, structural domains, GTEx eGene tissues, others
^cIncluding genomic annotations sourced from ENCODE, FANTOME5, BLUEPRINT Epigenome, Roadmap Epigenomics, The Cancer Genome Atlas, UCSC, others

ISSN: 1756-994X