Table 2
Tool/Resource | Analysis Objective | Number of Signatures or Datasets | Number of Samples Analyzed | Input | Output | Interface and Requirements | Runtime |
|---|---|---|---|---|---|---|---|
SaVanT | Visualization of molecular signatures across samples | 10,985 signatures | 1–150 samples | Gene expression matrix (gene symbols and values) | Interactive heatmap | Website/Browser | 75 s (50 samples, 25,219 genes, 4729 signatures, with ANOVA) |
GSEA | Identification of significant or differential gene sets and signatures | User-defined; MSigDB supported (up to 18,026 gene sets) | Two or more biological states (with replicates) | Expression dataset and phenotype data | Enrichment plots and lists | Java Archive Download | 4Â min (50 samples, 4729 signatures, 9096 genes, 1000 permutations) |
BubbleGUM | Extraction and visualization of molecular signatures and gene sets | User-defined; MSigDB supported (up to 18,026 gene sets) | 2+ samples | GCT file (expression dataset) and phenotype data | Graphical plots | Java Archive Download | 5Â min (13 samples, 75 signatures, 1000 permutations) |
GSVA | Estimation of variation in pathway and signature genes across samples | User-defined; MSigDB supported (up to 18,026 gene sets) | 2+ samples | Gene expression matrix and gene set data | Score matrix of enrichment scores | R package (Bioconductor) | 3Â min (30 samples, 100 gene sets, 20,000 genes) |
PLAGE | Quantification of pathway activity across samples | 400 pathways from KEGG | 2+ samples | Gene expression matrix | Heatmap of pathway activity levels | Website/Browser | N/A (Could not access website) |
ssGSEA | Determine enrichment of a gene set within dataset | User-defined; MSigDB supported (up to 18,026 gene sets) | 2+ samples | GCT file with expression estimates | Matrix of enrichment projections | R package (or via browser using GenePattern) | 2Â min (50 samples, 326 gene sets, 10,100 genes) |