RegNetwork is developed based on 25 databases, among which 17 of them provide the regulatory relationship information and 8 of them are supporting databases containing annotation and other necessary information in order to derive the regulatory relationships.
| Database | Description | Species | Website |
|---|---|---|---|
| BioGrid | BioGRID is an online interaction repository with data compiled through comprehensive curation efforts | Mouse | http://thebiogrid.org/ |
| Ensembl | Ensembl is to provide a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other vertebrates and model organisms | Human and mouse | http://www.ensembl.org |
| HPRD | HPRD is a curated human protein-protein interaction database | Human | http://www.hprd.org |
| IntAct | IntAct is a database system of molecular interaction data. All interactions are derived from literature curation or direct user submissions | Mouse | http://www.ebi.ac.uk/intact/ |
| KEGG | KEGG is a widely used pathway database resource for understanding high-level linkage functions and utilities of biological system | Human and mouse | http://www.genome.jp/kegg/ |
| MicroT | DIANA-microT is a combined computational-experimental approach predicts mouse microRNA targets | Human and mouse | http://www.microrna.gr/microT |
| miRanda | miRanda is a miRNA target prediction method based on dynamic programming algorithm | Human and mouse | http://www.microrna.org |
| miRBase | miRBase database is a searchable database of published miRNA sequences and annotation | Human and mouse | http://www.mirbase.org/ |
| miRecords | miRecords is a resource for animal miRNA-target interactions. The validated targets component is used, which is a large, high-quality database of experimentally validated miRNA targets | Human and mouse | http://miRecords.umn.edu/miRecords |
| miRTarBase | miRTarBase is a database which curates experimentally validated microRNA-target interactions | Human and mouse | http://miRTarBase.mbc.nctu.edu.tw/ |
| PicTar | PicTar is a computational method for identifying common targets of microRNAs | Human and mouse | http://pictar.mdc-berlin.de/ |
| STRING | STRING is a database of known and predicted protein interactions | Mouse | http://www.string-db.org |
| Tarbase | Tarbase collectes available miRNA targets derived from all contemporary experimental techniques (gene specific and high-throughput) | Human and mouse | http://www.microrna.gr/tarbase |
| TargetScan | TargetScan is an algorithm to predict biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA | Human and mouse | http://www.targetscan.org/ |
| TransmiR | TransmiR is a transcription factor-microRNA regulation database | Human and mouse | http://202.38.126.151/hmdd/mirna/tf/ |
| TRED | Transcriptional Regulatory Element Database (TRED) is an integrated repository repository for both cis- and trans- regulatory elements in mammals. It contains the curated regulations between TF and target gene | Human and mouse | http://rulai.cshl.edu/TRED/ |
| UCSC | The University of California, Santa Cruz Genome Browser is a database of genomic sequence and annotation data for a wide variety of organisms | Human and mouse | http://genome.ucsc.edu |
| Database | Description | Species | Website |
|---|---|---|---|
| FANTOM | Functional Annotation Of Mammalian genome and is an international research consortium to assign functional annotations to the full-length complementary DNAs (cDNAs) | Human and mouse | http://fantom.gsc.riken.jp/ |
| GenBank | A comprehensive database developed by NCBI, NIH, which contains publicly available nucleotide sequences for more than 250,00 formally described species | Human and mouse | http://www.ncbi.nlm.nih.gov/genbank/ |
| JASPAR | An open-access database of annotated, matrix-based transcription factor binding site (TFBS) profiles for multicellular eukaryotes | Human and mouse | http://jaspar.genereg.net/ |
| Liftover | A UCSC tool converts genome coordinates and genome annotation files between assemblies | Mouse | http://genome.ucsc.edu/cgi-bin/hgLiftOver |
| MicroCosm | MicroCosm Targets (formerly miRBase Targets) is a web resource containing computationally predicted targets for microRNAs across many species | Human and mouse | http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/v5/ |
| RefSeq | RefSeq provides a non-redundant collection of sequences representing genomic data, transcripts and proteins | Human and mouse | http://www.ncbi.nlm.nih.gov/refseq/ |
| TRANSFAC | Transfac database is a manually curated database of eukaryotic transcription factors, their genomic binding sites (TFBS) and DNA binding profiles | Human and mouse | http://www.gene-regulation.com/pub/databases.html |
| UniProt | UniProt is a catalog of information on proteins and it is a central repository of protein sequence and function | Human and mouse | http://www.uniprot.org/ |