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MIT 7 013 - Lecture Notes

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1STARTSTARTFOUNDATIONSFOUNDATIONSHowHow--to 1to 1FORMATIONFORMATIONHowHow--to 2to 2SYSTEMSSYSTEMSPROBLEMSPROBLEMSFuture ofFuture ofBIOCHEM GENETICS CELL BIO.MOL. BIOSTEM CELLS,CLONINGREC. DNACELL TYPE3DSTRUCTUREFERTILI-ZATIONSYSTEMSVIRUSESIMMUNELIFELIFENERVOUSCANCER2CTCCTTCGTATTACTCATTCAGCTCTTCCTCTGATAGCAGTGAATTTTCGAGGGTCACGTCGTGACTCATATGCTTTCTTGTTCCGTTTCGTTTCGAGATGACAAAAAACTGGTCATTTTTTCCGTTAAGTGCAACTCACAGCAGTATCGGCCGCTGAGAAATGCCCGGACAAATTTTTTTGAGCCGGATTGGTCACCGTTTCTTTCTTCGGCGCGGCTTCCCATTCCCGTCCATCCAAAAAAATCTACCTATATAAATCGACTTTTCACCTCTAAAGGCAGTTTATTCCTTGTATGTCCTTTAAGTACAGTTAATAACGAGCAATTTTTTTTTTTTTTTTTAGCCATCTACCCATCAACTTGTACACTCGTTACCATGTCAACCACAGCATCCACGCCTTCATCTTTACGTCATTTGATTTCTATAAAAGATCTTTCTGATGAAGAATTC3CTCCTTCGTATTACTCATTCAGCTCTTCCTCTGATAGCAGTGAATTTTCGAGGGTCACGTCGTGACTCATATGCTTTCTTGTTCCGTTTCGTTTCGAGATGACAAAAAACTGGTCATTTTTTCCGTTAAGTGCAACTCACAGCAGTATCGGCCGCTGAGAAATGCCCGGACAAATTTTTTTGAGCCGGATTGGTCACCGTTTCTTTCTTCGGCGCGGCTTCCCATTCCCGTCCATCCAAAAAAATCTACCTATATAAATCGACTTTTCACCTCTAAAGGCAGTTTATTCCTTGTATGTCCTTTAAGTACAGTTAATAACGAGCAATTTTTTTTTTTTTTTTTAGCCATCTACCCATCAACTTGTACACTCGTTACCATGTCAACCACAGCATCCACGCCTTCATCTTTACGTCATTTGATTTCTATAAAAGATCTTTCTGATGAAGAATTCArg3 Genomic DNA (beginning)4Observing gene expression in living cellswww.singerlab.orgNucleoplasmCytoplasmPeroxisomes5Imaged every 2.5 minutes for 4 hrsCyan FP-laciDNAYellow FP-MS2RNACyan FP-peroxisomesProtein6CTCCTTCGTATTACTCATTCAGCTCTTCCTCTGATAGCAGTGAATTTTCGAGGGTCACGTCGTGACTCATATGCTTTCTTGTTCCGTTTCGTTTCGAGATGACAAAAAACTGGTCATTTTTTCCGTTAAGTGCAACTCACAGCAGTATCGGCCGCTGAGAAATGCCCGGACAAATTTTTTTGAGCCGGATTGGTCACCGTTTCTTTCTTCGGCGCGGCTTCCCATTCCCGTCCATCCAAAAAAATCTACCTATATAAATCGACTTTTCACCTCTAAAGGCAGTTTATTCCTTGTATGTCCTTTAAGTACAGTTAATAACGAGCAATTTTTTTTTTTTTTTTTAGCCATCTACCCATCAACTTGTACACTCGTTACCATGTCAACCACAGCATCCACGCCTTCATCTTTACGTCATTTGATTTCTATAAAAGATCTTTCTGATGAAGAATTCArg3 Genomic DNA (beginning)7InputClustering data reveals patternsRows are genesColumns are expression values at time points 1 – 30(synthetic data)8InputClustering data reveals patternsRows are genesColumns are expression values at time points 1 – 30(synthetic data)9InputClusteredClustering data reveals patternsRows are genesColumns are expression values at time points 1 – 30(synthetic data)10Clustering expression data from synchronized cells reveals cell cycle dependant genesRed - gene upGreen - gene downtime 1 - 24gene 1..............gene 80011What graphical model best encodes this data?12ChromosomalPosition (bp)266000265500 266500 267000 267500 268000 268500 269000 269500 270000SIP4 --> ARG3 -->GCN4 FoldEnrichment(IP/WCE)5101520253035ORF LocationHigh-resolution view of Gcn4/genome interaction13CTCCTTCGTATTACTCATTCAGCTCTTCCTCTGATAGCAGTGAATTTTCGAGGGTCACGTCGTGACTCATATGCTTTCTTGTTCCGTTTCGTTTCGAGATGACAAAAAACTGGTCATTTTTTCCGTTAAGTGCAACTCACAGCAGTATCGGCCGCTGAGAAATGCCCGGACAAATTTTTTTGAGCCGGATTGGTCACCGTTTCTTTCTTCGGCGCGGCTTCCCATTCCCGTCCATCCAAAAAAATCTACCTATATAAATCGACTTTTCACCTCTAAAGGCAGTTTATTCCTTGTATGTCCTTTAAGTACAGTTAATAACGAGCAATTTTTTTTTTTTTTTTTAGCCATCTACCCATCAACTTGTACACTCGTTACCATGTCAACCACAGCATCCACGCCTTCATCTTTACGTCATTTGATTTCTATAAAAGATCTTTCTGATGAAGAATTCArg3 Coding SequenceGCN4 binding site1473 modules 401 genes 51


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MIT 7 013 - Lecture Notes

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