CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse
1 Center for Molecular Systems Biology, University of Torino, Via Accademia Albertina, 13 - I-10123 Torino, Italy
2 CIBIO-Centre for Integrative Biology, University of Trento, Via delle Regole 101, I-38100 Trento, Italy
3 Department of Oncological Sciences, c/o Institute for Cancer Research and Treatment (IRCC), School of Medicine, University of Torino, Str. Prov. 142 Km. 3.95, I-10060 Candiolo, Italy
4 Molecular Biotechnology Center, University of Torino, Via Nizza 52, I-10126 Torino, Italy
5 Systems Biology Lab, Institute for Cancer Research and Treatment (IRCC), School of Medicine, University of Torino, Str. Prov. 142 Km. 3.95, I-10060 Candiolo, Italy
BMC Bioinformatics 2010, 11:435 doi:10.1186/1471-2105-11-435Published: 23 August 2010
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.
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.