Computational systems biology  
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Database, Web Server and Software


miR2GO is a computational tool for the assessment of functional impacts of genetic and somatic mutations in miRNAs. The first function of this web server, miRmut2GO, allows users to analyze the changes of target genes caused by miRNA mutations and view the functional impacts of these changes in a gene ontology graph. This web server can also be used for analyzing the differences and similarities between the functions of different miRNAs. Different miRNAs perform different functions because they bind to different sets of target genes. The second function of the web server, miRpair2GO, allows users to perform comparative gene ontology analysis for the target gene sets of different miRNAs.  (Reference)


Bayesian Network Web Server


The Bayesian Network Web Server (BNW) is a comprehensive web server for Bayesian network modeling of biological data sets. It is designed so that users can quickly and seamlessly upload a dataset, learn the structure of the network model that best explains the data, and use the model to understand and make predictions about relationships between the variables in the model. Many real world data sets, including those used to create genetic network models, contain both discrete (e.g., genotypes) and continuous (e.g., gene expression traits) variables, and BNW allows for modeling of these hybrid data sets. (Reference)


SomamiR Database


A comprehensive resource that integrates several types of data for use in investigating the impact of somatic and germline mutations on miRNA function in cancer. The database contains somatic mutations that may create or disrupt miRNA target sites and integrates these somatic mutations with germline mutations within the same target sites, genome-wide and candidate gene association studies of cancer, and functional annotations that link genes containing mutations with cancer. Additionally, the database contains a collection of germline and somatic mutations in miRNAs and their targets that have been experimentally shown to impact miRNA function and have been associated with cancer. (Reference)


PolymiRTS Database


Linking polymorphisms in microRNA target sites with complex traits. Polymorphism in microRNA Target Site (PolymiRTS) is a database of naturally occurring DNA variations in putative microRNA (miRNA) target sites. This database characterizes PolymiRTS as a new class of sequence variants underlying gene expression traits and/or higher order mammalian traits. (Reference)




A CTCF binding site database for characterization of vertebrate genomic insulators. The database is a comprehensive collection of experimentally identified and computationally predicted CTCF binding sites. It is also a resource for studying insulators and their roles in demarcating functional genomic domains and regulating gene expression. (Reference)




A web tool to predict whether a nonsynonymous single nucleotide polymorphism (nsSNP) has a deleterious effect. nsSNPAnalyzer extracts structural and evolutionary information from a query nsSNP and uses a machine learning method called Random Forest to predict the nsSNP's phenotypic effect. (Reference)




A Gene Ontology tool to construct and visualize gene relation networks. Directed acyclic graphs are also generated to show the hierarchical structure of the Gene Ontology tree. (Reference)


Gifi Array Analyzer


A Java program for interpreting microarray data in the context of existing biological knowledge. It implements Homogeneity Analysis, a graphical multivariate statistical method for analyzing categorical data, to Integrate the analysis of microarray data and gene functional classification data. (Reference)






An integrative computational tool for genetical genomics.