Statistics (Release 2017-12-07)

RegenDbase contains gene and miRNA expression data from 15 experiments in 3 organisms. The data was last updated on December 7, 2017.

Organism Experiments Genes Transcripts/miRNAs miRNA Target Predictions
Expressed Total Expressed Total
Ambystoma mexicanum 4 16,838 16,838 24,754 24,754 0
Caenorhabditis elegans 0 0 48,139 0 59,162 98,252
Danio rerio 9 26,033 34,241 49,448 58,601 947,547
Homo sapiens 0 0 66,782 0 216,847 6,382,886
Mus musculus 2 19,854 51,939 53,319 120,579 3,306,714

Data Sources

RegenDbase integrates data from these excellent scientific resources:

Data Source Release References
Affymetrix Amby001 GeneChip AMBY_001a520165F PubMed: 17241119
Affymetrix Amby002 GeneChip AMBY_002a520748F PubMed: 22485136
ArrayExpress PubMed: 23193272
BioCyc 2016-10-26
BioGRID 3.4.141 PubMed: 16381927
Ensembl 86 PubMed: 24316576
Entrez Gene 2016-10-26 PubMed: 21115458
Gene Ontology 2016-10-26 PubMed: 10802651
GEO PubMed: 11752295
KEGG 2016-10-26
miRBase 21 PubMed: 21037258
NCBI BioSystems 2016-10-26 PubMed: 19854944
NCBI Taxonomy 2016-10-26 PubMed: 18940862
PubMed: 18940867
OrthoDB 9 PubMed: 23180791
Pathway Interaction Database 2016-10-26
PubMed 2016-10-28
Reactome 2016-10-26
Superfamily 1.75 PubMed: 11697912
WikiPathways 2016-10-26


The RNA-Seq and microarray gene- and miRNA-expression experiments included in RegenDbase are pre-analyzed.

To nominate an experiment for inclusion in RegenDbase, please contact us.




RegenDbase integrates Ensembl genes and miRBase miRNAs for humans, mice, nematodes, and zebrafish, but we create our own gene vocabulary for axolotls....

Gene Annotations

GO annotations are integrated from Ensembl.

Pathway annotations are integrated from NCBI BioSystems, and include annotations from BioCyc, KEGG, Pathway Interaction Database, Reactome, and WikiPathways.

miRNA Target Predictions

RegenDbase creates new miRNA target predictions for certain organisms when we integrate new releases of Ensembl and miRBase.

miRNA target predictions are created by RegenDbase using the default parameters of the miRanda software.

Accession Identifiers

Wherever possible, data integrated into RegenDbase are identified by the unique accession identifiers assigned by their original source. Where such IDs are not available, however, RegenDbase assigns its own.

RegenDbase accession IDs are composed of a prefix based on the data type, followed by a series of digits (e.g., "REGENG:627"):

Accession Prefix Data Type
REGENE: Experiments
REGENG: Genes that are not mappable to Ensembl (e.g., axolotl genes)
REGENR: References that not represented in PubMed
REGENS: Experiment samples