Maran Homepage Maran Users Guide Maran Preprint of Application Note Example Input File AQBC Homepage AQBC Information Page AQBC Preprint of Paper Example Input File Example Input File GO4G Homepage GO4G Help Example Input File Intergenic Select Homepage INCLUSive Help Example Input File TOUCAN Homepage TOUCAN Documentation Toucan Preprint of Paper Example Input File MotifSampler Homepage INCLUSive Help MotifSampler Preprint of Paper 1 MotifSampler Preprint of Paper 2 Example Input File MotifScanner Homepage INCLUSive Help Toucan Preprint of Paper
INCLUSive Logo
Welcome to the INCLUSive web portal. INCLUSive is a suit of algorithms and tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements. The tools allow for normalization, filtering and clustering of microarray data, functional scoring of gene clusters, sequence retrieval and detection of known and unknown regulatory elements. All tools are available via different web pages and as web services. A UDDI registry (and browser) is available that catalogues and describes the services.
Cite us To reference INCLUSive, please cite this paper:
Coessens,B., Thijs,G., Aerts,S., Marchal,K., De Smet,F., Engelen,K., Glenisson,P., Moreau,Y., Mathys,J., and De Moor,B. (2003)
INCLUSive: a web portal and service registry for microarray and regulatory sequence analysis. Nucleic Acids Res., 31: 3468-3470
Mailing List If you like to be informed about INCLUSive updates and changes, you should join the INCLUSive mailing list
INCLUSive Flow Chart (Clickable map)
Click the image elements for more information
INCLUSive Web Services
General Toucan service router:
Web Application Stand Alone Executable Info
Link Description Download General References
MARAN MARAN is a web-based application for normalizing micro-array data. MARAN comprises a generic ANOVA model, an option for Loess fitting prior to ANOVA analysis and a module for selecting genes with signifcantly changing expression.   manual [6]
AQBC Adaptive quality-based clustering of gene expression profiles.     [5]
Functional Scoring:
GO4G GO4G calculates which Gene Ontology terms are statistically over-represented within a set of (related) genes.      
Sequence Retrieval:
Intergenic Select This web page allows you to download intergenic sequences. For a given gene the upstream nucleotide sequence is downloaded from NCBI GenBank.      
Sequence Comparison:
Avid/Vista   download   [4] [8]
Motif Detection:
MotifSampler The Motif Sampler tries to find over-represented motifs in the upstream region of a set of co-regulated genes. This motif finding algorithm uses Gibbs sampling to find the position probability matrix that represents the motif. download help [7] [9] [10]
MotifScanner MotifScanner is a program that can be used to screen DNA sequences with precompiled motif models. The algorithm is based on a probabilistic sequence model in which motif are assumed to be hidden in a noisy background sequence. To model the background we use higher-order Markov models. On this site precompiled background models are available for many organisms. download help [1] [11]
FootPrinter   download manual [2] [3]
[1] Aerts, S., Thijs, G., Coessens, B., Staes, M., Moreau, Y., De Moor, B. (2003) TOUCAN: Deciphering the Cis-Regulatory Logic of Coregulated Genes. Nucleic Acids Res., 31: 1753-1764
[2] Blanchette, M., Schwikowski, B., and Tompa, M. (2002) Algorithms for Phylogenetic Footprinting. Journal of Computational Biology, 9: 211-223
[3] Blanchette, M. and Tompa, M. (2002) Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting. Genome Research, 12: 739-748
[4] Bray, N., Dubchak, I. and Pachter, L. (2003) AVID: A Global Alignment Program. Genome Research, 13: 97
[5] De Smet, F., Mathys, J., Marchal, K., Thijs, G., De Moor, B., Moreau, Y. (2002) Adaptive quality-based clustering of gene expression profiles. Bioinformatics, 18: 735-746
[6] Engelen, K., Coessens, B., Marchal, K., De Moor, B. (2003) MARAN: normalizing micro-array data. Bioinformatics, 19: 893-894
[7] Marchal, K., Thijs, G., De Keersmaecker, S., Monsieurs, P., De Moor, B., Vanderleyden, J. (2003) Genome-specific higher-order background models to improve motif detection. Trends Microbiol, 11: 61-66
[8] Mayor C., Brudno M., Schwartz J. R., Poliakov A., Rubin E. M., Frazer K. A., Pachter L. S. and Dubchak I. (2000) VISTA: Visualizing Global DNA Sequence Alignments of Arbitrary Length. Bioinformatics, 16: 1046
[9] Thijs, G., Lescot, M., Marchal, K., Rombauts, S., De Moor, B., Rouzé, P., Moreau, Y. (2001) A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling. Bioinformatics, 17: 1113-1122
[10] Thijs, G., Marchal, K., Lescot, M., Rombauts, S., De Moor, B., Rouzé, P., Moreau, Y. (2002) A Gibbs Sampling method to detect over-represented motifs in upstream regions of coexpressed genes. J. Comput. Biol., Special Issue RECOMB 2001, 9: 447-464
[11] Wingender, E., Chen, X., Hehl, R., Karas, H., Liebich, I., Matys, V., Meinhardt, T., Prüß, M., Reuter, I. and Schacherer, F. (2000) TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res., 28: 316-319

Design: Bert Coessens
Last Update: 2003/04/17