CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse.
BACKGROUND
Transcription Factors (TFs) and microRNAs (miRNAs) are key players for gene expression regulation in higher eukaryotes. In the last years, a large amount of bioinformatic studies were devoted to the elucidation of transcriptional and post-transcriptional (mostly miRNA-mediated) regulatory interactions, but little is known about the interplay between them.


METHODS
Here we describe a dynamic web-accessible database, CircuitsDB, supporting a genome-wide transcriptional and post-transcriptional regulatory network integration, for the human and mouse genomes, based on a bioinformatic sequence-analysis approach. In particular, CircuitsDB is currently focused on the study of mixed miRNA/TF Feed-Forward regulatory Loops (FFLs), i.e. elementary circuits in which a master TF regulates an miRNA and together with it a set of Joint Target protein-coding genes. The database was constructed using an ab-initio oligo analysis procedure for the identification of the transcriptional and post-transcriptional interactions. Several external sources of information were then pooled together to obtain the functional annotation of the proposed interactions. Results for human and mouse genomes are presented in an integrated web tool, that allows users to explore the circuits, investigate their sequence and functional properties and thus suggest possible biological experiments.


CONCLUSIONS
We present CircuitsDB, a web-server devoted to the study of human and mouse mixed miRNA/TF Feed-Forward regulatory circuits, freely available at: http://biocluster.di.unito.it/circuits/
Friard
Olivier
O
Center for Molecular Systems Biology, University of Torino, Via Accademia Albertina, 13 - I-10123 Torino, Italy.
Re
Angela
A
Taverna
Daniela
D
De Bortoli
Michele
M
Corá
Davide
D
D000818:Animals; D001483:Base Sequence; D030541:Databases, Genetic; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D016678:Genome; D006801:Humans; D020407:Internet; D051379:Mice; D035683:MicroRNAs / Q000378:metabolism*; D009369:Neoplasms / Q000235:genetics; D016415:Sequence Alignment; D014157:Transcription Factors / Q000378:metabolism*
D035683:MicroRNAs; D014157:Transcription Factors