miRNA regulatory module inference bioinformatics tools| Gene expression analysis

miRNA regulatory module inference software tools | Transcription analysis

Recognizing the modular organization of biological networks has greatly advanced our understanding of complex cellular systems. However, little is known about the modules that exist in miRNA-gene regulation systems, and even less is known about these modules’ role in specific biological processes and key regulation assemblies. Identifying functional miRNA-gene regulatory modules is a challenging task for several reasons. (i) One gene can be regulated by multiple miRNAs, and one miRNA can regulate a large number of genes. (ii) The miRNA–mRNA target relationships differ among tissues and conditions. (iii) Although miRNAs physically interact with mRNAs, ultimately miRNA regulation affects the quantities of proteins in cells rather than the quantities of mRNAs. (iv) The genomic data are generally noisy and incomplete.

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Mirin / MicroRNA Regulatory Modules in Protein-Protein Interaction Network

An online tool for identification of micorRNA-mediated module which is formed by protein-protein interactions (PPIs). Mirin integrates microRNA regulations and PPIs with microRNA/mRNA expression data to identify the perturbed microRNA regulatory modules and reveals their functional roles in specific biological conditions.

WormNet

Hosts a network-assisted hypothesis-generating server for C. elegans. WormNet includes a base gene network, which substantially improved predictions of RNAi phenotypes. The server generates various gene network-based hypotheses using three complementary network methods: (i) a phenotype-centric approach to ‘find new members for a pathway’; (ii) a gene-centric approach to ‘infer functions from network neighbors’ and (iii) a context-centric approach to ‘find context-associated hub genes’, which is a method to identify key genes that mediate physiology within a specific context.

SNMNMF

Serves for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules. SNMNMF is a program that presents the following characteristics: (1) integrates prior knowledge such as a gene interaction network as a constraint on the solution space; (2) allows users to upload several different types of data; (3) and provides sparse solutions. Moreover, this tool can be used for many problems involving heterogeneous data sources.

Mirsynergy

Detects synergistic miRNA regulatory modules. Mirsynergy operates in two stages: it first forms microRNA regulatory modules (MiRMs) based on co-occurring microRNA (miRNA) targets and then expands each MiRM by greedily including (excluding) mRNAs into (from) the MiRM to maximize the synergy score, which is a function of miRNA-mRNA and gene-gene interactions.

StarBioTrek

Allows measurement of pathway activity and crosstalk among pathways. StarBioTrek was developed for the identification of a network of dependent pathways and their regulatory miRNAs. It was used for revealing microRNA (miRNAs) that can regulate, in a coordinated way, networks of gene pathways and permitted to identify pairwise pathways for breast cancer (BC) subtypes able to discriminate BC versus normal samples.

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