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BI420 – Introduction to Bioinformatics Gene Expression Analysis Gabor T. Marth Department of Biology, Boston College [email protected] Gene expression Why study gene expression? Which genes are active • at different developmental stages? • in cells of different tissues? • at different time points in the same cell? • cells under different environmental conditions? • between normal and cancerous cells? What are expression microarrays? Expression microarrays – “physical appearance” Microarray construction cDNA preparation Expression assay Expression microarray movie DNA microarray chip animation: http://www.bio.davidson.edu/Courses/genomics/chip/chip.html Chip readout – absolute expression and ratio Chip readout – relative transcription Chip readout – example Time course experiments Experiment: measuring gene expression as oxygen gets depleted in yeast grown in a closed container Time course data Data analysis – normalization • balance fluorescent intensities of two dyes • adjust for differences in experimental conditions Normalization Log2 transformation Double or half expression now has the same magnitude Clustering – intro • Why: if the expression pattern for gene B is similar to gene A, maybe they are involved in the same or related pathway • How: Re-order expression vectors in the data set so that similar patterns are together Clustering – numerical Clustering – visual Hierarchical clustering: pair-wise similarity Hierarchical clustering: cluster construction Clustering – large example Next two classes Chapter 7. Chapter 8. Application of microarrays: classification of cancers Microarrays to detect genome copy # Protein identification Protein separation by 2D gel eletrophoresis Protein identification mass spectrometry Protein function identification protein chips: identification of proteins that bind specific chemicals Thanks Expression informatics slides courtesy of: Olga Troyanskaya, Ph.D. Department of Computer Science Lewis-Sigler Institute for Integrative Genomics Princeton University