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 |
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 |
DOI | ||
Ensembl | 86 | PubMed: 24316576 |
Entrez Gene | 2016-10-26 | PubMed: 21115458 |
Gene Ontology | 2016-10-26 | PubMed: 10802651 |
GEO | PubMed: 11752295 | |
InterPro | ||
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 |
UniProt | ||
WikiPathways | 2016-10-26 | |
WormBase | ||
ZFIN |
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....
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.
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.
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 |