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miRNA regulatory modules inference software tools | Pathway 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…
MFSN
Algorithm

MFSN MiRNA-miRNA Functional Synergistic Network

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…

JoungEtAl2007
Algorithm

JoungEtAl2007

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…

DICORE
Algorithm

DICORE DIscovering COllective group RElationships

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…

Yoon,De…
Algorithm

Yoon,De Micheli2005

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…

LiuEtAl2010
Algorithm

LiuEtAl2010

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…

Joung,Fei2009
Algorithm

Joung,Fei2009

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…

PIMiM
Algorithm

PIMiM Protein Interaction-based MicroRNA Modules

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…

Mirsynergy
Desktop

Mirsynergy

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…

TranEtAl2008
Algorithm

TranEtAl2008

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…

LiuEtAl2009
Algorithm

LiuEtAl2009

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…

miRnalyze
Dataset

miRnalyze

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…

ProteoMirExpres…
Web

ProteoMirExpress

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…

BCM
Desktop

BCM BiCliques Merging

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.…

PmmR
Dataset

PmmR Putative microRNA-microRNA Regulations

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…

Mirin
Web

Mirin MicroRNA Regulatory Modules in Protein-Protein Interaction Network

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…

ZhangEtAl2012
Algorithm

ZhangEtAl2012

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,…

SNMNMF
Desktop

SNMNMF

A data integration framework to identify the miRNA-gene regulatory co-modules.…

A data integration framework to identify the miRNA-gene regulatory co-modules. SNMNMF integrates miRNA and gene expression profiles from the same patients, miRNA-gene networks, and gene interaction…

iSubgraph
Desktop

iSubgraph

A tool to discover patterns of miRNAs and their target genes, observed…

A tool to discover patterns of miRNAs and their target genes, observed frequently up- or down-regulated in a group of patients. iSubgraph is capable to detect cooperative regulation of miRNAs and…

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