Table 1 Overview of the analysis and visualization tools available in EucGenIE
Category / Tool name | Description | Tool status |
|---|---|---|
Gene Search tools | Â | Â |
GeneList | Search and save genes to a gene list | Customized for EucGenIE |
Cross-species GeneList | Create a PlantGenIE (cross-species) gene list using ortholog information | New tool |
Genome tools | Â | Â |
BLAST | Performs sequence homology searches | GenIE-Sys |
JBrowse | Browse genomics data on genome browser | GenIE-Sys |
ChrDiagram | Plots the location of genes in the active gene list in chromosomes | GenIE-Sys |
SeqSearch | Extracts sequence information for genes in the active gene list | Improved (GenIE-Sys) |
Expression tools | Â | Â |
exNet | Displays co-expression networks based on precalculated transcriptional expression networks | Improved (GenIE-Sys) |
exImage | Visualizes single gene expression profiles using an electronic fluorescent pictograph (eFP) | Improved (GenIE-Sys) Customized for EucGenIE |
exPlot | Generates line graphs of expression profiles across samples in the selected experiment | GenIE-Sys |
exHeatmap | Represents expression profiles for genes in the active gene list using a heatmap representation | Improved (GenIE-Sys) |
exMatch | Finds groups of genes with the desired expression profile | New tool |
Analysis tools | Â | Â |
Venn | Generates an interactive Venn diagram of the gene lists stored in EucGenIE | New tool |
Enrichment | Performs enrichment analysis for gene ontology (GO) categories, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and Protein family (Pfam) domains within a gene list | Improved (GenIE-Sys) |
Population Genomics tools | Â | Â |
qtlXplorer | Performs on-the-fly systems genetics data queries using an interactive version of Circos | New tool |