mirConnX: condition-specific mRNA-microRNA network integrator

Abstract

mirConnX is a user-friendly web interface for inferring, displaying and parsing mRNA and microRNA (miRNA) gene regulatory networks. mirConnX combines sequence information with gene expression data analysis to create a disease-specific, genome-wide regulatory network. A prior, static network has been constructed for all human and mouse genes. It consists of computationally predicted transcription factor (TF)-gene associations and miRNA target predictions. The prior network is supplemented with known interactions from the literature. Dynamic TF- and miRNA-gene associations are inferred from user-provided expression data using an association measure of choice. The static and dynamic networks are then combined using an integration function with user-specified weights. Visualization of the network and subsequent analysis are provided via a very responsive graphic user interface. Two organisms are currently supported: Homo sapiens and Mus musculus. The intuitive user interface and large database make mirConnX a useful tool for clinical scientists for hypothesis generation and explorations. mirConnX is freely available for academic use at http://www.benoslab.pitt.edu/mirconnx.

Figure 1.

Overview of the integrated analysis in mirConnX. Visualization is achieved with the use of Cytoscape Web v0.7.2 (25). Feed-forward loops are displayed on a separate tab. Links to external databases provided for every coding gene or miRNA. Statistical analysis on GO pathway (45) overrepresentation in a user-selected set of genes will be added soon.

Figure 2.

Snapshot of the glioblastoma case study output. An example search for the downstream targets of miR-21, a key player in glioblastoma development, is shown in the middle.