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A database of MicroRNA / Transcription Factor Regulatory Circuits in Human and Mouse

Welcome to Circuits DB, a resource devoted to the identification and analysis of mixed MicroRNA / Transcription Factor Regulatory Circuits in the Human and Mouse genomes.

Promoters and 3'-UTRs are thought to control the expression of coding genes mainly in response to transcription factors (TF) and microRNAs. In particular, several methods exist to elucidate TF-related and microRNA-related regulatory networks, but comparable information is lacking to explicitly connect them.

This web-site supports a study of a genome-wide transcriptional and post-transcriptional regulatory network integration, in the human and mouse genomes, based on a bioinformatic sequence-analysis work.

In particular, this web-site is currently focused on the study of a particular type of connection between transcriptional and post-transcriptional interactions: the MicroRNA / Transcription Factor Feed-Forward Regulatory Loops (FFLs), i.e. elementary circuits in which a master transcription factor regulates a microRNA and together with it a set of joint target protein-coding genes. A catalogue of mixed Feed-Back Regulatory Loops (FBLs) is reported as well.

FFL schema

These circuits were assembled throught a bioinformatic sequence-analysis pipeline, applied to the human and mouse genomes (Re et al., Mol Biosyst. 2009 - PMID: 19603121 and Friard et al., BMC Bioinformatics. 2010 - PMID: 20731828).

In addition to that, we recently presented and discussed:
- a database of mixed microRNA / Transcription Factor Feed-Forward regulatory Loops having MYC as master regulator and characterized completely by experimentally supported regulatory interactions, in human (MYC FFLs).
- an in-depth study of intronic miRNA-mediated self-loops (iMSLs).

This web-site represents a dynamic interface to the FFLs database. It is divided in six sections:

FFL
You can explore our dataset of mixed FFLs, for human and mouse. Entry point can be a TF of interest, a miRNA or a gene.
This is the main access point to our database. Direct access to the FFL dataset and additional documentation can be found through the links
on the left sidebar.
Transcriptional Network
You can also explore our transcriptional network, for human and mouse. Entry points can be a TF of interest, a gene or a DNA oligo.
Post-Transcriptional Network
You can also explore our post-transcriptional network, for human and mouse. Entry points can be a miRNA of interest, a gene or a DNA oligo.
Documentation
You can browse a documentation page, describing the content and the utility of CircuitsDB. A complete working example is also reported.
Download
You can access all the data sets contained in CircuitsDB in plain text format. In particular, you can download the complete catalogue of mixed FFLs
and the catalogue of FBLs for the human and mouse genomes.
References
You can access a list of the main data sources interrogated for the construction of CircuitsDB.