BBE7120Ed01 - Systems Biology Systems Biology Transcriptome...

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Systems Biology Academic year 2009 - 2010 1 Systems Biology Transcriptome Transcriptome analysis analysis Transcriptional networks Prof. Dr. Pierre Hilson VIB Department of Plant Systems Biology University of Ghent Academic year 2009 Academic year 2009-2010 2010 Outline - Transcriptomics applications - Gene ontology and beyond - Mapping of transcription units Mi f t i t il tk - Mapping of transcriptional networks Study of network motifs - Study of network motifs
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Systems Biology Academic year 2009 - 2010 2 Expression profiling ¤ Transcriptome or genome-wide expression analysis aims to – Monitor the expression levels of “all” genes Monitor the expression levels of all genes – Correlate expression profiles with biological activity ¤ Applications Applications – Identifying genetic networks and pathways Id tif i th f ti f k Identifying the function of unknown genes – Diagnose physiological (disease) states ¤ First application of high throughput/large scale biology – Massively parallel data acquisition – Novel methods for large scale data analysis Typical Eucaryotic Transcriptome ¤ A typical eukaryotic cells has – Few abundantly expressed genes Few abundantly expressed genes – Great number of poorly expressed genes Abundance Copies Number of Copies class per cell genes transcripts abundant > 1,000 4 50.000 intermediate 100 - 1,000 500 100.000 scarce 1 -100 11.000 150.000 Total 11.500 300.000 Reprinted from: “The Cell ”
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Systems Biology Academic year 2009 - 2010 3 Transcriptome Analysis Platforms ¤ DNA sequencing based methods – DNA sequencing of individual transcripts to count the number of times a transcript is present – Initially limited resolution but with the next generation of sequencing platforms this is rapidly changing ¤ Array-based hybridization methods – Hybridization to gene-specific DNA probes arrayed on a solid support (membranes or glass) Has become the most performant and most widely used platform – Has become the most performant and most widely used platform ¤ DNA fragment analysis based methods PCR based amplification of DNA fragments derived from mRNA or cDNA – PCR-based amplification of DNA fragments derived from mRNA or cDNA whereby • Each DNA fragment represents a different mRNA – Currently primarily used for not (yet) sequenced species Cluster Analysis and Display of Genome-wide Expression Patterns Eisen et al. (1998) PNAS 95, 14863 ¤ Landmark paper presenting a method for analyzing and representing genome-wide expression data – Cluster analysis of data using standard statistical algorithms to arrange genes according to similarity in expression pattern Graphically display of data conveying clustering and – Graphically display of data conveying clustering and expression data in a form intuitive for biologists ¤ The logic for organizing gene expression data is – To group genes with similar patterns of expression – To use a mathematical description of similarity • Statistic captures similarity in "shape" but places no emphasis on the Statistic captures similarity in shape but places no emphasis on the magnitude of the measurements
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BBE7120Ed01 - Systems Biology Systems Biology Transcriptome...

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