LecturesPart12

LecturesPart12 - Computational Biology, Part 12 Expression...

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Unformatted text preview: Computational Biology, Part 12 Expression array cluster analysis Robert F. Murphy, Shann-Ching Chen Robert F. Murphy, Shann-Ching Chen Copyright Copyright 2004-2009. 2004-2009. All rights reserved. All rights reserved. Gene Expression Microarray A popular method to A popular method to detect mRNA expression level since reported by since reported by Pat Brown Laboratory in 1995 and by Pat Brown Laboratory in 1995 and by Affymetrix in 1996 Affymetrix in 1996 Different technologies for producing the Different technologies for producing the microarray chips and different approaches microarray chips and different approaches for analyzing microarray data for analyzing microarray data Should carefully process and analyze the data Should carefully process and analyze the data What is gene expression and why is it important? Gene Expression in different organs A highly specific process in which a gene is switched highly specific process in which a gene is switched on, and therefore begins production of its protein. on, and therefore begins production of its protein. Sources : image from the Cancer Genome Anatomy Project (CGAP), Conceptual Tour, July 21, 2000. http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/MolBioReview/gene_expression.html Gene Expression in single organ Gene expression also varies within a certain Gene expression also varies within a certain type of cell at different points in time. type of cell at different points in time. Sources : image from the Cancer Genome Anatomy Project (CGAP), Conceptual Tour, July 21, 2000. http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/MolBioReview/gene_expression.html Microarray raw data Label mRNA from one sample with a red Label mRNA from one sample with a red fluorescence probe (Cy5) and mRNA from fluorescence probe (Cy5) and mRNA from another sample with a green fluorescence another sample with a green fluorescence probe (Cy3) probe (Cy3) Hybridize to a chip with specific DNAs Hybridize to a chip with specific DNAs fixed to each well fixed to each well Measure amounts of green and red Measure amounts of green and red fluorescence fluorescence Flash animations: PCR http://www.maxanim.com/genetics/PCR/PCR.htm Microarray http://www.bio.davidson.edu/Courses/genomics/chip/chip.html Example microarray image Microarray is a technology to globally ( simultaneously detecting thousands of genes ) detect mRNA expression level. mRNA expression microarray data for 9800 genes (gene number shown vertically) for 0 to 24 h (time shown horizontally) after addition of serum to a human cell line that had been deprived of serum (from http://genome- www.stanford.edu/serum) Data extraction Adjust fluorescent intensities using Adjust fluorescent intensities using standards (as necessary) standards (as necessary) Calculate ratio of red to green fluorescence Calculate ratio of red to green fluorescence Convert to log Convert to log 2 and round to integer and round to integer...
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LecturesPart12 - Computational Biology, Part 12 Expression...

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