Table 1.
A summary of XGR characteristics for tasks achieved and runtime required
| Functions | Tasks achieved | Runtimea |
|---|---|---|
| Enrichment analysis | ||
| xEnricher | A template for enrichment analysis | ~40 |
| xEnricherGenes | Gene-based enrichment analysis using a wide variety of ontologiesb | ~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 ontologiesb | ~60 |
| xGRviaGenomicAnno | Annotation analysis using a wide variety of genomic annotationsc | ~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