Laboratorium voor Computationele Biologie, Centrum voor Menselijke Erfelijkheid (KULeuven)
Stage-onderwerp 2012-2013:Tools for cis-regulatory sequence analysis in Galaxy
The Laboratory of Computational Biology has developed several tools and methods for cis-regulatory sequence analysis, such as TOUCAN, ModuleSearcher, i-cisTarget, and i-Regulon. The goal of this project is to create Galaxy plugins for several of these methods, to test them, and to create workflows that combine several methods using in-house generated data on cancer and on Drosophila eye development.
Samenvatting eindwerk 2012-2013: Development of Galaxy plugins for regulatory motif analysis
Understanding how the expression of the genes is regulated at the transcriptional level remains a great challenge. While a lot of regulatory information is now becoming available thanks to the Next Generation Sequencing (NGS) technologies, analysis methods are still not perfect. For example, Chromatin Immunoprecipitation sequencing (ChIP-seq) can give information about the binding of a given transcription factor or about the chromatin changes. The challenge is to analyze this data efficiently and to acquire reliable information about regulatory elements like Transcription Factors (TF) and Transcription Factor Binding Sites (TFBS). These can suppress or enhance gene expression by controlling DNA transcription. With this information regulatory networks can be created. Bioinformatics methods for cis-regulatory sequence analysis work by searching for regulatory motifs around the transcription start site of co-expressed genes. In the Laboratory of Computational Biology (LCB) a tool has been developed to predict motifs and Cis-Regulatory Modules (CRM) in Drosophila, and this tool is available through a web interface called i-cisTarget. This method uses a region-based approach hereby expanding the regulatory search space allowing more distant regulatory elements to be found. The goal of this project is to create a new interface for i-cisTarget using the Galaxy framework. Our Galaxy plugin will be applicable for more species and will allow more flexible analyses by combining i-cisTarget with follow-up and visualization tools like Cluster-Buster and ToucanMap. Galaxy is an open web-based platform designed for data intensive biomedical research. For example, i-cisTarget can be used to detect the TFs regulating differentially expressed genes derived from RNA-seq data. In addition, several other supportive Galaxy plugins were developed to retrieve a dataset that can be used as input for i-cisTarget, to fetch the predicted target genes, and to detect and visualize the binding sites of an enriched motif. All together, these Galaxy plugins have made regulatory sequence analysis user-friendly and they will be made available to the scientific community.
Samenvatting eindwerk 2011-2012: iRegulon: a Cytoscape plugin for the discovery and visualization of gene regulatory networks
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