Biomedical subjects

Stein Aerts

Publications and source records attributed to Stein Aerts.

12 recordsLinked to original sources

PubMed2006

Prediction of a key role of motifs binding E2F and NR2F in down-regulation of numerous genes during the development of the mouse hippocampus.

BACKGROUND: We previously demonstrated that gene expression profiles during neuronal differentiation in vitro and hippocampal development in vivo were very similar, due to a conservation of the important second singular value decomposition (SVD) mode (Mode 2) of expression. The conservation of Mode 2 suggests that it reflects a regulatory mechanism conserved between the two systems. In either dataset, the expression vectors of all the genes form two large clusters that differ in the sign of the contribution of Mode 2, which for the majority of them reflects the difference between down- or up-regulation. RESULTS: In the current work, we used a novel approach of analyzing cis-regulation of gene expression in a subspace of a single SVD mode of temporal expression profiles. In the putative upstream regulatory sequences identified by mouse-human homology for all the genes represented in either dataset, we searched for simple features (motifs and pairs of motifs) associated with either sign of the loading of Mode 2. Using a cross-system training-test set approach, we identified E2F binding sites as predictors of down-regulation of gene expression during hippocampal development. NR2F binding sites, for the transcription factors Nr2f/COUP and Hnf4, and also NR2F_SP1 pairs of binding sites, were predictors of down-regulation of expression both during hippocampal development and neuronal differentiation. Analysis of another dataset, from gene profiling of myoblast differentiation in vitro, shows that the conservation of Mode 2 extends to the differentiation of mesenchymal cells. This permitted the identification of two more pairs of motifs, one of which included the CDE/CHR tandem element, as features associated with down-regulation both in the differentiating myoblasts and in the developing hippocampus. Of the features we identified, the E2F and CDE/CHR motifs may be associated with the cycling progenitor cell status, while NR2F may be related to the entry into differentiation along the neuronal pathway. CONCLUSION: Our results constitute the first prediction of an expression pattern from the genomic sequence for the developing mammalian brain, and demonstrate a potential for the analysis of gene regulation in a subspace of a single SVD mode of expression.

Amino Acid Motifs↗

PubMed2006

Gene prioritization through genomic data fusion.

The identification of genes involved in health and disease remains a challenge. We describe a bioinformatics approach, together with a freely accessible, interactive and flexible software termed Endeavour, to prioritize candidate genes underlying biological processes or diseases, based on their similarity to known genes involved in these phenomena. Unlike previous approaches, ours generates distinct prioritizations for multiple heterogeneous data sources, which are then integrated, or fused, into a global ranking using order statistics. In addition, it offers the flexibility of including additional data sources. Validation of our approach revealed it was able to efficiently prioritize 627 genes in disease data sets and 76 genes in biological pathway sets, identify candidates of 16 mono- or polygenic diseases, and discover regulatory genes of myeloid differentiation. Furthermore, the approach identified a novel gene involved in craniofacial development from a 2-Mb chromosomal region, deleted in some patients with DiGeorge-like birth defects. The approach described here offers an alternative integrative method for gene discovery.

Algorithms↗

PubMed2006

Identification of conserved modes of expression profiles during hippocampal development and neuronal differentiation in vitro.

Gene expression profiles can be regarded as sums of simpler modes, analogous to the modes of a vibrating violin string. Decomposition of temporal gene expression profiles into modes by singular value decomposition (SVD) was reported before, but the question as to what degree the SVD modes can be interpreted in terms of biology remains open. We report and compare the results of SVD of published datasets from hippocampal development, neuronal differentiation in vitro, and a control time-series hippocampal dataset. We demonstrate that the first SVD mode reflects the magnitude of expression, interpretable on the Affymetrix platform. In the datasets from gene profiling of hippocampal development and neuronal differentiation, the second mode reflects a monotonous change in expression, either up- or down-regulation, in the time course of experiment. We demonstrate that the top two SVD modes are conserved between datasets and therefore, likely reflect properties of the underlying system (gene expression in hippocampus) rather than of a particular experiment or dataset. Our results also indicate that the magnitude of expression, and the direction of change in expression during hippocampal development, are uncorrelated, suggesting that they are regulated by largely independent mechanisms.

Animals↗

PubMed2005

TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis.

We present the second and improved release of the TOUCAN workbench for cis-regulatory sequence analysis. TOUCAN implements and integrates fast state-of-the-art methods and strategies in gene regulation bioinformatics, including algorithms for comparative genomics and for the detection of cis-regulatory modules. This second release of TOUCAN has become open source and thereby carries the potential to evolve rapidly. The main goal of TOUCAN is to allow a user to come to testable hypotheses regarding the regulation of a gene or of a set of co-regulated genes. TOUCAN can be launched from this location: http://www.esat.kuleuven.ac.be/~saerts/software/toucan.php.

Algorithms↗

PubMed2004

Comprehensive analysis of the base composition around the transcription start site in Metazoa.

BACKGROUND: The transcription start site of a metazoan gene remains poorly understood, mostly because there is no clear signal present in all genes. Now that several sequenced metazoan genomes have been annotated, we have been able to compare the base composition around the transcription start site for all annotated genes across multiple genomes. RESULTS: The most prominent feature in the base compositions is a significant local variation in G+C content over a large region around the transcription start site. The change is present in all animal phyla but the extent of variation is different between distinct classes of vertebrates, and the shape of the variation is completely different between vertebrates and arthropods. Furthermore, the height of the variation correlates with CpG frequencies in vertebrates but not in invertebrates and it also correlates with gene expression, especially in mammals. We also detect GC and AT skews in all clades (where %G is not equal to %C or %A is not equal to %T respectively) but these occur in a more confined region around the transcription start site and in the coding region. CONCLUSIONS: The dramatic changes in nucleotide composition in humans are a consequence of CpG nucleotide frequencies and of gene expression, the changes in Fugu could point to primordial CpG islands, and the changes in the fly are of a totally different kind and unrelated to dinucleotide frequencies.

AT Rich Sequence↗

PubMed2004

A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes.

SUMMARY: The implementation of a genetic algorithm is described that provides a fast method of searching for the optimal combination of transcription factor binding sites in a set of regulatory sequences. AVAILABILITY: The algorithm can be used transparently as a web service from within the Toucan software. Toucan can be accessed at http://www.esat.kuleuven.ac.be/~saerts/software/toucan.php. A standalone version of the software is available upon request.

Algorithms↗

PubMed2004

Identification of IGFBP-6 as a significantly downregulated gene by beta-catenin in desmoid tumors.

Desmoid tumors (aggressive fibromatosis) are locally invasive soft tissue tumors in which beta-catenin-mediated TCF-3-dependent transcription is activated. To provide more insight into the pathophysiology of these tumors, expression profiles were generated using oligonucleotide arrays (Affymetrix). In total, 69 differentially expressed genes were identified in desmoids compared to normal fibroblasts (fascia) from the same patients. The differential expression of a selection of genes was confirmed using RT-PCR and Northern blotting. We further evaluated the insulin-like growth factor-binding protein 6 (IGFBP-6), a gene that was consistently downregulated in all desmoids tested. Promotor studies and electromobility shift assays revealed two functional beta-catenin/TCF-responsive elements in the human IGFBP-6 promoter. These findings suggest that IGFBP-6 is directly downregulated by the beta-catenin/TCF complex in desmoid tumors, and imply a role for the IGF axis in the proliferation of desmoid tumors.

Animals↗

PubMed2003

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.

Algorithms↗

PubMed2003

Toucan: deciphering the cis-regulatory logic of coregulated genes.

TOUCAN is a Java application for the rapid discovery of significant cis-regulatory elements from sets of coexpressed or coregulated genes. Biologists can automatically (i) retrieve genes and intergenic regions, (ii) identify putative regulatory regions, (iii) score sequences for known transcription factor binding sites, (iv) identify candidate motifs for unknown binding sites, and (v) detect those statistically over-represented sites that are characteristic for a gene set. Genes or intergenic regions are retrieved from Ensembl or EMBL, together with orthologs and supporting information. Orthologs are aligned and syntenic regions are selected as candidate regulatory regions. Putative sites for known transcription factors are detected using our MotifScanner, which scores position weight matrices using a probabilistic model. New motifs are detected using our MotifSampler based on Gibbs sampling. Binding sites characteristic for a gene set--and thus statistically over-represented with respect to a reference sequence set--are found using a binomial test. We have validated Toucan by analyzing muscle-specific genes, liver-specific genes and E2F target genes; we have easily detected many known binding sites within intergenic DNA and identified new biologically plausible sites for known and unknown transcription factors. Software available at http://www.esat.kuleuven.ac. be/ approximately dna/BioI/Software.html.

Algorithms↗

PubMed2003

Comparison and meta-analysis of microarray data: from the bench to the computer desk.

The upcoming availability of public microarray repositories and of large compendia of gene expression information opens up a new realm of possibilities for microarray data analysis. An essential challenge is the efficient integration of microarray data generated by different research groups on different array platforms. This review focuses on the problems associated with this integration, which are: (1) the efficient access to and exchange of microarray data; (2) the validation and comparison of data from different platforms (cDNA and short and long oligonucleotides); and (3) the integrated statistical analysis of multiple data sets.

Databases, Genetic↗

PubMed2003

Gene profiling of hippocampal neuronal culture.

We performed mRNA expression profiling of mouse primary hippocampal neurones undergoing differentiation in vitro. We show that 2314 genes significantly changed expression during neuronal differentiation. The temporal resolution of our experiment (six time points) permits us to distinguish between gene expression patterns characteristic for the axonal and for the dendritic stages of neurite outgrowth. Cluster analysis reveals that, in the process of in vitro neuronal differentiation, a high level of expression of genes involved in the synthesis of DNA and proteins precedes the up regulation of genes involved in protein transport, energy generation and synaptic functions. We report in detail changes in gene expression for genes involved in the synaptic vesicle cycle. Data for other genes can be accessed at our website. We directly compare expression of 475 genes in the differentiating neurones and the developing mouse hippocampus. We demonstrate that the program of gene expression is accelerated in vitro as compared to the situation in vivo. When this factor is accounted for, the gene expression profiles in vitro and in vivo become very similar (median gene-wise correlation 0.787). Apparently once the cells have taken a neuronal fate, the further program of gene expression is largely independent of histological or anatomical context. Our results also demonstrate that a comparison across the two experimental platforms (cDNA microarrays and oligonucleotide chips) and across different biological paradigms is feasible.

Animals↗

PubMed2003

Computational detection of cis -regulatory modules.

MOTIVATION: The transcriptional regulation of a metazoan gene depends on the cooperative action of multiple transcription factors that bind to cis-regulatory modules (CRMs) located in the neighborhood of the gene. By integrating multiple signals, CRMs confer an organism specific spatial and temporal rate of transcription. RESULTS: Based on the hypothesis that genes that are needed in exactly the same conditions might share similar regulatory switches, we have developed a novel methodology to find CRMs in a set of coexpressed or coregulated genes. The ModuleSearcher algorithm finds for a given gene set the best scoring combination of transcription factor binding sites within a sequence window using an A(*)procedure for tree searching. To keep the level of noise low, we use DNA sequences that are most likely to contain functional cis-regulatory information, namely conserved regions between human and mouse orthologous genes. The ModuleScanner performs genomic searches with a predicted CRM or with a user-defined CRM known from the literature to find possible target genes. The validity of a set of putative targets is checked using Gene Ontology annotations. We demonstrate the use and effectiveness of the ModuleSearcher and ModuleScanner algorithms and test their specificity and sensitivity on semi-artificial data. Next, we search for a module in a cluster of gene expression profiles of human cell cycle genes. AVAILABILITY: The ModuleSearcher is available as a web service within the TOUCAN workbench for regulatory sequence analysis, which can be downloaded from http://www.esat.kuleuven.ac.be/~dna/BioI.

Algorithms↗