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.
Source text:
(Zhang et al., 2011) A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules. Bioinformatics.
Allows users for in-depth analysis of individual miRNAs in the context of…
Allows users for in-depth analysis of individual miRNAs in the context of synergistic surroundings. MFSN is a computational method to identify significantly functional synergistic miRNA pairs via…
Permits to identify miRNA modules from their predicted miRNA targets as well as…
Permits to identify miRNA modules from their predicted miRNA targets as well as their expression data sets. The algorithm of Joung et al. is a population-based probabilistic search method. This model…
Identifies miRNA-mRNA regulatory modules (MMRMs) and hence reveals miRNA-mRNA…
Identifies miRNA-mRNA regulatory modules (MMRMs) and hence reveals miRNA-mRNA regulatory relationships from heterogeneous data. DICORE is an effective computational framework to reveal correct group…
Permits to identify important patterns hidden in the complex interactions. The…
Permits to identify important patterns hidden in the complex interactions. The algorithm of Yoon and De Micheli is a computational method to predict miRNA regulatory modules (MRMs) or groups of…
Allows discovering the functional miRNA regulatory modules (FMRMs). The…
Allows discovering the functional miRNA regulatory modules (FMRMs). The algorithm of Liu et al. is a method that integrates heterogeneous datasets, including expression profiles of both miRNAs and…
Detects the role of miRNAs in various interesting biological processes and…
Detects the role of miRNAs in various interesting biological processes and environmental stimuli. The algorithm of Joung and Fei provides a framework to efficiently hypothesize associations between…
Extends the regression framework of GroupMiR by using an additional type of…
Extends the regression framework of GroupMiR by using an additional type of data: protein interactions. PIMiM is a method for inferring condition-specific regulation of miRNAs and for identifying…
Detects synergistic miRNA regulatory modules. Mirsynergy operates in two…
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…
Performs a comprehensive analysis of the combinatorial nature of gene…
Performs a comprehensive analysis of the combinatorial nature of gene regulation by detecting rules that identify a set of miRNAs associated with genes. The algorithm of Tran et al. is a…
Incorporates heterogeneous information to discover biologically relevant…
Incorporates heterogeneous information to discover biologically relevant miRNA–mRNA groups. The algorithm of Liu et al. is a computational method for identifying functional regulatory miRNA–mRNA…
Predicts putative miRNA targets in cellular signaling pathways directly through…
Predicts putative miRNA targets in cellular signaling pathways directly through identifying involved genes in those pathways. miRnalyze is a web app that integrates two of the most important…
Integrates proteomic and mRNA expression data together to infer miRNA-centered…
Integrates proteomic and mRNA expression data together to infer miRNA-centered regulatory networks. With both types of high-throughput data from the users, ProteoMirExpress is able to discover not…
A method to predict miRNA regulatory modules (MRMs) based on bicliques merging.…
A method to predict miRNA regulatory modules (MRMs) based on bicliques merging. BCM exploits the miRNA/mRNA expression profiles, target site predictions as well as the gene-gene interactions.…
Facilitates the search of the putative miRNA–miRNA regulations. PmmR…
Facilitates the search of the putative miRNA–miRNA regulations. PmmR retrieves the corresponding regulated and regulating miRNAs with scores by selecting a miRNA name. Scores are nothing but the…
An online tool for identification of micorRNA-mediated module which is formed…
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…
Infers functional miRNA– mRNA regulatory modules (FMRMs), which consist of…
Infers functional miRNA– mRNA regulatory modules (FMRMs), which consist of miRNAs, mRNAs and expression types in each biological class type. The algorithm of Zhang et al. is a probabilistic model,…
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