INCLUSive: a web portal and service registry for microarray and regulatory sequence analysis

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.

[1]  Kathleen Marchal,et al.  MARAN: Normalizing Micro-array Data , 2003, Bioinform..

[2]  Kathleen Marchal,et al.  Functional bioinformatics of microarray data: from expression to regulation , 2002, Proc. IEEE.

[3]  Kathleen Marchal,et al.  A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling , 2001, Bioinform..

[4]  L. Stein.  Creating a bioinformatics nation , 2002, Nature.

[5]  Xin Chen,et al.  TRANSFAC: an integrated system for gene expression regulation , 2000, Nucleic Acids Res..

[6]  Bart De Moor,et al.  Evaluation of the Vector Space Representation in Text-Based Gene Clustering , 2002, Pacific Symposium on Biocomputing.

[7]  Jason E. Stewart,et al.  Design and implementation of microarray gene expression markup language (MAGE-ML) , 2002, Genome Biology.

[8]  Kathleen Marchal,et al.  Adaptive quality-based clustering of gene expression profiles , 2002, Bioinform..

[9]  B. De Moor,et al.  Toucan: deciphering the cis-regulatory logic of coregulated genes. , 2003, Nucleic acids research.

[10]  Kathleen Marchal,et al.  MARAN : normalizing microarray data , 2003 .

[11]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[12]  Kathleen Marchal,et al.  PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences , 2002, Nucleic Acids Res..

[13]  B. De Moor,et al.  Genome-specific higher-order background models to improve motif detection. , 2003, Trends in microbiology.

[14]  Kathleen Marchal,et al.  A Gibbs sampling method to detect over-represented motifs in the upstream regions of co-expressed genes , 2001, RECOMB.

[15]  Kathleen Marchal,et al.  INCLUSive: INtegrated Clustering, Upstream sequence retrieval and motif Sampling , 2002, Bioinform..

[16]  Alistair G. Rust,et al.  Ensembl 2002: accommodating comparative genomics , 2003, Nucleic Acids Res..