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Identifiers and Annotation
For mouse, human and rat, benchsiDE embeds identifier-to-symbol tables:
| Species | Source | Identifier types |
|---|---|---|
| Mouse | MGI (MRK_ENSEMBL.rpt and MGI_EntrezGene.rpt) | Ensembl, Entrez |
| Human | HGNC complete set | Ensembl, Entrez |
| Rat | RGD GENES_RAT | Ensembl, Entrez |
Select the species on the start screen and click Use built-in annotation. The source and its citation are added to the methods text. The tables are subsets of the source files, redistributed under the providers' licenses (MGI and RGD: CC BY 4.0; HGNC: CC0 1.0).
If some identifiers are not found, the start screen reports the number and offers Download unmapped IDs. Typical causes are retired identifiers, non-coding features absent from the annotation release, or identifiers from another species.
Supply a two-column file (identifier, symbol) for species or identifier types not covered by the built-in tables. The file is cited as a user-supplied mapping.
The Gene Explorer links each gene to external resources appropriate to its species (Ensembl, NCBI Gene, MGI, RGD, GeneCards). Links open in a new tab; no expression data is sent.
Gene matching between datasets is described in Cross-dataset comparison and Orthologs and homology families.
Start
Data preparation
Statistics
- Differential expression
- Covariates and pairing
- Multiple contrasts
- Statistical power
- Gene-set testing
- Discovery screen
- Patterns and clustering
- Heatmaps
- Co-expression
Comparing datasets
Output
Background