RegNetwork: Regulatory Network Repository of Transcription Factor and microRNA Mediated Gene Regulations

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.

Regulatory Relationship Databases

Database Description Species Website
BioGrid BioGRID is an online interaction repository with data compiled through comprehensive curation efforts Mouse
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
HPRD HPRD is a curated human protein-protein interaction database Human
IntAct IntAct is a database system of molecular interaction data. All interactions are derived from literature curation or direct user submissions Mouse
KEGG KEGG is a widely used pathway database resource for understanding high-level linkage functions and utilities of biological system Human and mouse
MicroT DIANA-microT is a combined computational-experimental approach predicts mouse microRNA targets Human and mouse
miRanda miRanda is a miRNA target prediction method based on dynamic programming algorithm Human and mouse
miRBase miRBase database is a searchable database of published miRNA sequences and annotation Human and mouse
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
miRTarBase miRTarBase is a database which curates experimentally validated microRNA-target interactions Human and mouse
PicTar PicTar is a computational method for identifying common targets of microRNAs Human and mouse
STRING STRING is a database of known and predicted protein interactions Mouse
Tarbase Tarbase collectes available miRNA targets derived from all contemporary experimental techniques (gene specific and high-throughput) Human and mouse
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
TransmiR TransmiR is a transcription factor-microRNA regulation database Human and mouse
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
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

Supporting Databases

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
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
JASPAR An open-access database of annotated, matrix-based transcription factor binding site (TFBS) profiles for multicellular eukaryotes Human and mouse
Liftover A UCSC tool converts genome coordinates and genome annotation files between assemblies Mouse
MicroCosm MicroCosm Targets (formerly miRBase Targets) is a web resource containing computationally predicted targets for microRNAs across many species Human and mouse
RefSeq RefSeq provides a non-redundant collection of sequences representing genomic data, transcripts and proteins Human and mouse
TRANSFAC Transfac database is a manually curated database of eukaryotic transcription factors, their genomic binding sites (TFBS) and DNA binding profiles Human and mouse
UniProt UniProt is a catalog of information on proteins and it is a central repository of protein sequence and function Human and mouse