Stem Cell Biology and Bioinformatics Tools

Syllabus

• Course syllabus in English

Recommended reading

• From Human Molecular Genetics Stem Cell Review supplement (http://hmg.oxfordjournals.org/content/vol17/R1/) there are a number of interesting review articles. These 3 represent the most useful for the course.
• Gene W. Yeo, Nicole Coufal, Stefan Aigner, Beate Winner, Jonathan A. Scolnick, Maria C.N. Marchetto, Alysson R. Muotri, Christian Carson, and Fred H. Gage Multiple layers of molecular controls modulate self-renewal and neuronal lineage specification of embryonic stem cells Hum. Mol. Genet. 2008 17: R67-R75; doi:10.1093/hmg/ddn065
• Victoria V. Lunyak and Michael G. Rosenfeld Epigenetic regulation of stem cell fate Hum. Mol. Genet. 2008 17: R28-R36; doi:10.1093/hmg/ddn149
• Lingyi Chen and George Q. Daley Molecular basis of pluripotency Hum. Mol. Genet. 2008 17: R23-R27; doi:10.1093/hmg/ddn050
• Regulatory networks define phenotypic classes of human stem cell lines Supplementary data at www.stemcellmatrix.org - see speficically the cytoscape visualisation of the PluriNet of genes.
• Joern Toedling, Oleg Sklyar and Wolfgang Huber Ringo – an R/Bioconductor package for analyzing ChIP-chip readouts [[ http://www.biomedcentral.com/1471-2105/8/443][ BMC Bioinformatics 2007, *8 *: 221 doi:10.1186/1471-2105-8-221]]**

Prepare your own microarray data:

• In order to get the most from this course, we recommend that you use your own microarray data, or data that is relevant to your research project. You can search the literature for a suitable experiment in your area of interest. For example see ArrayExpress, or GEO for public repositories of microarrays. Otherwise, gene lists from specific papers of interest will also be a good start for analysis.
• We are currently experiencing problems with the computer setup so may not be able to run your own data - we are working on the problem and will try our best to enable this.

Analysis links:

• Ensembl - Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes.
• ArrayExpress - ArrayExpress is a public repository for transcriptomics data, which is aimed at storing MIAME- and MINSEQE- compliant data in accordance with MGED recommendations. The ArrayExpress Warehouse stores gene-indexed expression profiles from a curated subset of experiments in the repository.
• ArrayExpress Atlas - ArrayExpress Atlas of Gene Expression is a semantically enriched database of meta-analysis based summary statistics over the entire ArrayExpress Data Warehouse, servicing queries for condition-specific gene expression patterns (e.g. genes over-expressed in a particular tissue or disease state) as well as broader exploratory searches for biologically interesting genes/samples.
• DAVID - DAVID Identify enriched biological themes, particularly GO terms, Discover enriched functional-related gene groups, Cluster redundant annotation terms, Visualize genes on BioCarta & KEGG pathway maps
• PathwayCommons - Pathway Commons is a collection of publicly available pathways from multiple organisms. It provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language. Access is via a web portal for browsing, query and download. Database providers can share their pathway data via a common repository and avoid duplication and reduce software development costs. Bioinformatics software developers can increase efficiency by sharing software components. Pathways include biochemical reactions, complex assembly, transport and catalysis events, and physical interactions involving proteins, DNA, RNA, small molecules and complexes.
• cytoscape - Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.
• CellDesigner - CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation system proposed by Kitano, and are stored using the Systems Biology Markup Language (SBML), a standard for representing models of biochemical and gene-regulatory networks. Networks are able to link with simulation and other analysis packages through Systems Biology Workbench (SBW).