MIT6_047f08_lec20_note20

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Unformatted text preview: MIT OpenCourseWare http://ocw.mit.edu 6.047 / 6.878 Computational Biology: Genomes, Networks, Evolution Fall 2008 For information about citing these materials or our Terms of Use, visit: http://ocw.mit.edu/terms . Genome wide study of gene regulation 6.047/6.878 Lecture 20 Lectured by P. Kheradpour, 11/13/08 Table of contents Genome wide study of gene regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 Gene expression patterns (motivation) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 Transcription factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 Experimental discovery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 Computational discovery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 Discovered motifs have functional enrichments . . . . . . . . . . . . . . . . . . . . . . . . . . 2 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 microRNAs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 The biology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 Computational miRNA discovery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 12 Drosophila genomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 Validation of the predicted miRNAs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 Additional signatures of mature miRNAs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 Prediction of binding sites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 Experimental approaches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 Computational approaches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 Phylogenetic footprinting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 Comparison with experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 Network level examination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 Gene expression patterns (motivation) Given the complex spatial and temporal regulation of gene expression [7], exemplified by recent studies on the mouse [21], and on Drosophila heart development [30], there is great impetus to identify the targets of regulatory factors in order to understand how such regulation is achieved....
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This note was uploaded on 09/24/2010 for the course EECS 6.047 / 6. taught by Professor Manoliskellis during the Fall '08 term at MIT.

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MIT6_047f08_lec20_note20 - MIT OpenCourseWare...

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