ABSTRACT
We implemented a framework called TXTGate that combines literature indices of selected public biological resources in a flexible text-mining system designed towards the analysis of groups of genes. By means of tailored vocabularies, term- as well as gene-centric views are offered on selected textual fields and MEDLINE abstracts used in LocusLink and the Saccharomyces Genome Database. Subclustering and links to external resources allow for in-depth analysis of the resulting term profiles.
Subject(s)
Gene Expression Profiling/methods , Information Storage and Retrieval/trends , Animals , Cluster Analysis , Databases, Genetic/statistics & numerical data , Disease Models, Animal , Gene Expression Profiling/statistics & numerical data , Gene Expression Regulation, Fungal/genetics , Gene Expression Regulation, Neoplastic/genetics , Genes, Fungal/genetics , Genes, Neoplasm/genetics , Genome, Fungal , Genome, Human , Humans , Information Storage and Retrieval/statistics & numerical data , MEDLINE/standards , MEDLINE/statistics & numerical data , Mice , Saccharomyces/genetics , Salivary Gland Neoplasms/genetics , VocabularyABSTRACT
INCLUSive is a suite of algorithms and tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements. The tools allow normalization, filtering and clustering of microarray data, functional scoring of gene clusters, sequence retrieval, and detection of known and unknown regulatory elements using probabilistic sequence models and Gibbs sampling. All tools are available via different web pages and as web services. The web pages are connected and integrated to reflect a methodology and facilitate complex analysis using different tools. The web services can be invoked using standard SOAP messaging. Example clients are available for download to invoke the services from a remote computer or to be integrated with other applications. All services are catalogued and described in a web service registry. The INCLUSive web portal is available for academic purposes at http://www.esat.kuleuven.ac.be/inclusive.
