Phenotype Genotype Host Vector Pathogen 1 Bacterial Viral - PDF document

It is like any other experiment! • You need to know your data/input sources What is a bioinformatics • You need to understand your methods and their assumptions experiment? • You need a plan to get from point A to point B • You need to understand your equipment • You need to be critical and understand potential sources of error • You need to interpret your results • Your results need to be reproduceable • Your results should be testable Infectious Disease Paradigm Remember the Goal Experimental systems Phenotype Genotype Host Vector Pathogen 1

Bacterial Viral Parasitic Host Genetics Immunology Know your data Genomics Microarray Proteomic >Pfa3D7|chr1_000035|2001.01.03|GENOMIC|Sanger CCAGTTTGTGATGTTTCTCCTTGTTGCACATAGCCACTTCCTTTCTTCCTCTGTTAAAAAAGCTCCTCTCCCCAGAATACTCCCTTGTAGCACCATGATTGAATGACCACTCTTTCTTAAGTGAACTTCTTGAAAAC TAGCTTGAATCCATCCTCTTCATTTCCTTACCTCTTATTTCAGTTTCAGCCTATTGCTGTCTAGCATATGATATATCTGCCATTCTGCATGTGATATATCTCAATGCCTGTCATCATTTCCAGCATTCCACCCTATA TGTGGCCTATATACCGCCATCTTCTGTCCCATGCTCTTACTGAAGTCTGCCTAGATTAGACCATTTTAAAGTCCATCACTACATACTTCTTCCTCTTCTGGTCCTTTAGCTTGATGGACACACCTGGTTTCATACTT ACTAATTATTGCATTTGGCAACTGTATTTACTACTTAAACCATTCTTTCACCCTTACGTGGTTTGGGTTGGCTGTCGCTCTCAGGAGTACCTGGCTAGCTTGGCTGCATGGTTTCCCTGCCAAAATAGATACAGGAA Typical 2 D gel GGGTAGTACCTCCTAGGGGATGCTATGCTTTTTGAGATAAGGCTCCTGGAAATAGGTGTCATCCAGTCTGAACCTATGAGAAATGGAGATCGCTTGAGATTATTGCCTACTTAAAGAACCTTAGTGAACTGTTCTAC TAGGATTTACTTTTCACAGCTCCTTGATGGGGAAAAAAAAAAATTACACATTCGAGTTCTTCCCTCAGGGATAAATACGAAAAACTTGTCCATCAGCTTAGCTAGAAGTTAGCAACCACAGACAGAAACTTTGTAAT ACTTTTTTTTTAAAGTTTTATAATATTCTTAGTTCTCATATTAGTTTTTTTTTTTCATCTTTTCCCATTTTTTTGTGATTATAAAACTTTTTACATTGGAATTGTTCTGTTACTGTGTGGAGCAAAAAATAAGAGGG GAAATTGTTTAGACCTTTTATACTAAGTCTTAGTATATCCAGAGGGGAGTGTAGGTGGTGGCAGCTTTACAATGGAAAGGAAACGTGGGGAGTCCCCAGGACCTGCAGTCAATGAATAACAGGCTCCCTCCGTGACT GGTAAGAGAGTTTTGGGAGGTGAGTATAACATGACTCATTCAGGTTCTTTCTTGCTCTTTAATTTCTGTGATATTTTGCTGGTCTATGAAACTGATAAGCCTTAATGGTTGCAGTTTATTCTGACCCAGAGTTTATT TTCTAGTGATGCCTTTATTTTTTTGTTGGGATGTTGCTGGATAGTAAAGTAAAACTGAAGATCCTGGCCTTTCTCGTTCTCCTTCAAGAAAATGGGATTTCAGAAAACACTTGTCTTTAGCCTTCTCATGAAATTAA TTTCATAGACCTGTTTCTTGTTTTGATGGAACCCCTGTAGAGTTACCTAATATAAAGGTATATTAAGATTTTCTAGAGAAACAGAACCCATAGGCTAGATGAAGAGATAGATTTAAGAGGAGAGTTCTTGTAGGTGT TGGCTCACATGGTTATAAGGAAGTCCCATGATCTGTAGCCTGGAGAACCAGGACAGCTGGTGATGTGTTTCAGTCTAGGTTCAAAGGTCTGAGAGTCTGAGAATCAGGTGGACGGGAGGGTGTTAGTCCTGGGCTGG GTCTGAAAGCTTAAGAACTTAAGGCCGGATGTCTAGGGGCAGGAGACGAGTGTCTCAGCTCTAGCACAGAGCGAATTTGCCCTGCTGCCTCTTTGTTTATTCAGGCCCTCAGTGTATTGGAAGATGCCCACTTAAAG TAGGCAGTCTACTTAAAGAGGACCAGTCTACTTTGGTCTTCCCCAAAGTGGATTAGGGAGGATCATCTACTTTACTCAGTTATCAATTTAAGTGCTAATCTCTTCTGGAAATGCCCTCATAGACACACCCTGAAATA ATGGTTTACCAGCTATCTGGGCACCTCTTACTTTACATTCACAAGTAATGTTAACCATCACAACAGAGTAAAAAAACCTGTTGTTGTTGTTATTGTCTTGCTTTTTTAAAGGAGAGATTTATTTCTGCTGCTAGTTT AACTTCCTCCTAAAACTGGTTTGGTAATATTCGTGAACTCCCATGACTAGAGAAACTTCAGGTGTCTGTAGAGCTCTTTGACTTTCAGAACCGTGTTGCAAGTGTCCTTAACTGATTTGAAAGTTCTAATAACAACC AACGTTGGAATGTTGATCGTGTTCTAGGTGCTGTGCCAAATGCTCCCCGCATAACCTCTCACCTGATTGCTAAAACAGCTTTATGAGCTCCGTATTGTCTACATTTTACAGGAGTGCCAACTGAAGCCTGGACAAGT AAATTATCTTCTCAGGTTACACATAGGCTGCTGGGCCTGGCTTCTGGCCTTCAATTCTAACTATTGTTATTTTCATGAAAGTGACACCTTAAGTGCTTTCTTTGGTAGTGGTGTTGGGGTAAGCCTTTGTAGAACAG AACAGTTGTTACAGAAAACTTGTTTACATGGAAGCATTCCTTCAGCGATGACTGACAGACGGGAAAAGCAAAGTGCAGGTCGACCATCTCAAATATGAAAATGTGAAATCCAAAATGCTCCAAAATCCAAAACTTCT TGGGATTGACATGATGCTCATAGGAAATGCTCTTTGGAGCATTTTGGATTTTAGATTTTTGGGTTCGGGATGCTCAACCTGTAAGTATAATGCAAATATTCCAAATTCTGAAAAAAGGCGAAATCAGAAACACTTTT GGTCCCAGACATTTAGAATGAGGGCTATGCAACCTGTAACTGAGAATTTTTACCTAGTGCATATTATGTCCAAGTAACTAACAACTGTTGAAGGAAAGAATTTTAACATCCCATTTTACTCTCATTAAGTGGTTGTG GAAATGACCAATGGCATTTATACTTAGGTTTGTAACATCATCCATTTATTATACGGTCTTTCTTTGCTTATCTGCTGCATTCTTGAGATTGAAAATTTTATCCTGGAATAATAAATGACCCTATCTCAAACAGCTGC CATGTTAAGATGAATAAGAACATCATAGGGGGAGTAGATGCATTTTTGGGAGGCCTCCATCTGAAGTGACATGAATTCATAACACTCTAGTTCTGTCTACATGTCATGCTGTTACTAGGTGAGCAGGGAACTGTCAT TCCTACACCTTATTTAATAGAGGTGATCAGAATGGAGGATAAAGGGAAATAGCATGAGACTGTGAATGGATGTGGGGATTCTCATTGGTTTTGCTGCCAAGTAGAATCGTGTCACCTAGCAAATCACAACATTTCTG GCCTTCACTTTCCTGACTAGTAAAACGAGGTTTTTGAACTAGGCTGTCTTTACTGATTCTTTAACTGCTAAAGTTCTATGATTTTACATATGAAACCAAACCTAACAACATTGCTAACATGTATTTTTCAAAGCCAC AGAAGTTACATGCACATTTAATGAAGTTCCAGTGGCTTTATTAGAATTGGCTGATTGTACCATTATATTGCATTATAATAGCAAGGGTGAGGGTTGTTTACTTGTTCGGGGAAGGGGGGCATTGGGGCTACTTGTAC TTAAGCCTCAGGCCTGCCTGCTTCATGATCTTTGCTTGCCTTTTCTCACTACTAATTGCCCCTCACTTACAAGCTGAGACCTGCCCTCTTTCCCCTAGGGCTAATGCCTGTGTTGGGATCTTGAGCTCTCTTTTTGT TAACTGATTCTCTGTGTTTTTTTGTTTTTTTGTTTTTTTTTTGAGACGAGTCTCGCTGTGTCGCCCAAGCTGGAGCGCAGTGGTGTGATCTCTGCTCACTGAAACCTCTACCTGCCGGGTTCAAGCAATTCTCCTGC CTCAGCCTCCTGAGTAGCTGGGATTACAGGCATGCACCACCACGCCTGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGTCAGGCTGGTCTCAAACTCCTGACCTTGTGATCCGCCCACCTTG GCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCTGGCCCTCCTTTTTTCTTTTTTGGGACGGTGTGTGGCTCATTGCTTAGGCTGGATTGCAGTGGCACAATCTCGGCTTACTACAACCTCCGCCTTC CTGGTTCAAGTGATTCTTCTCCCTCGCTTCCCGAGTAGCTAGGATTACAGGCGCCCGCCACCATGCCCTGCTAATTTTGTATTTTTAGTAGAGACGAGGTTTCACCAAGTTGGTCTGGCTGGTCTTGAACTCCTGAC CTCAGGTGATCCACCCAACTTGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGCACCCGGCCATGTTAACTGGTTTTCTTTTTTTGTCCCTGAGTTCCTGTCTTTAGGATCTGAACACTTGATTTTTATT TATTTATTTATTTTTTTTGTTTGTGAAACTCGTTTCGCTTTTGTTGCCCAGGCTGTAGTGCAATGGCATGATCTCGGCTCACTGTGCAACCTCTGCCTTCTGGGTTCAAGCAATTCTCCTGCCCCACCCAGCCTCCT GAGTATCTGGGATTACAGGCTCCTGCCAGCACGCCCGGCTAATTTTTGTATTTTTTAGTAGAGATGGGGTTCACCACTTTGGCCTGGCTGGTCTTGAACTCCCGACCCCAGATGATCCGCTTGCCTCGGCCTGCCAA AGTGTTGGGATTACAGCTGTGAGCCACTGTCCCCGGCCTTTTTTTTTTTTTTTTAGATGGGGTCTTTTTCTATTGCCCAGGCTGGAGTGCAGTGGTTTGATCATAGCTCACTGTAGCCTTGAACTCCTGGGCTCAAA CAATCCCCCACCTCAGCCTCCCAAAGCGCTGGGATTATAGGCATGAGCTACCACACCCGGCCTGAACACTTGATCCCTTTTTTTTTTTTTTTTTTTTTTGAGACAGCAATGATGCGATCTTGGCTCACTGTAACGTA CGCCTCAAGTAGCTGGGATTATAGGCGCCCGCCACCATGCCTGGCCAATTTTTTTGGATTTTAGTAGAGACAGGGTTTCACCATGTTGGCCGGGCTGGTCTGGAACTCCTGACCTCAGGTGATCTTCCCGCCTTGGC TTCCGAAAATGGGATTACTGGCGTGAGCCACCGTGCCCGGCCTCACTGGAGCTCTTTTAATAGGTGAACTCTGGTTGCCCCTTTGCATGTCTCTTATTCCTTCCTCTGCTATAGGAATATAGGCTTTTAAACCCCAA CTCCGTGAGTAGACCAGCCTGCTTCTCTGAATTTCTGAGTACCAGGTGAACCTGCAGGGTGTCATGTCAGAAACAGAGACTTTTTTTTTTTATAGTGAAGATGTCCTTGATGACTGTGTATACAAATACACACACAT ACACACTTTTTAAAAAAAGTTAATTTCCAGACTTTATGGACAGTGTGCAGATTCTTTATTATATCACAGTGTTATTTTTCTTGCCTGCATTTCCCCCCACCTTCTATGGCTTTGCCTGTATTACCACATATTTATTA CAGAATCCTTTGACACCAGTGTTCTGGCTGATTCCCTGTCAACCCTCTGTTGTCTCCCTCTGTTCCCCACCTAACTCTCTCTAAGTGGGCAGGCTTGTTTTTGGTTATGATTCGCCCCAAAAGTTATAAAAGTACAT TTGGATCATAGTTGCCTTTGATGGTTTCTGCGGTAGAACCAGTGGTGCCAGTTAATTTCTTGAATGGCTGCCCCCATAAATTGGGAGTAGCTATTGGAAGTGCTTTGTGAGCTTATCAGGGAAATGACAGGACTGAA TAATGATCTGTCATGGGCATGGTATGGGGGGTGGTGGCACATGTGCCATCATTTGCCAGTGGCCCCGGAAGCCCAACACTCTGTTTATATATGTGTATTAATTGTTTCTTTGGTTGTCCAGCATTGGACTCATAATG GCCTTTTGTATATATCAGGGTTCCTCACCGTTTGAAGTAGAGTTTCCAATACCTACTTTAACATTGGCTCAGCCACTTATATTTACAAAAGGTCTCAAGATTTCTTACTGGTAGAATTATTTAGATTCTATACTTAA TATTAAGCAATTTCACCCTTGAGTCATAATTTCCAAAGTGTGCTCTCCCAGTATATTCTAATAGCGGTTCCCAGGATTTGGACCACGGACTGTATTGAGGAAAAATGCTGGTTGCTAGGTATTAAGAACTGATGTAA ATTAGTAAGAAAAGACAGATGATCCATTGAAAATGTGGTAAAATAATAATAGGTAATGTTTGCCGAGTGTGCCAGATCCTGTGGTAAGTGTTTTAAATGTTGTGTTGGTTGCTTTTCATAGTTCCCTAATGAGATCA TTATGATTATCCCTAATTTGTGCTTGAGGAAGTGAGGCACAGAAGCTCATTAAGTTCCCTGAGGTCACCCATACTTAAGTGATGGAACCAGGACTTGAGCCGAGTCAGCCCAACTCCAGAGCCTGTCCTCATAACCA ATGTGTTGTAAAGGTCAAAGGAGATTTCCGGATCTTCACAGAAAGGGAACACAAATTCACATTGACAGATATAAATTATTTTGAGGTACCGCTTTTCACTTCTGAGATTCAAGTGTGACTCTGGCAAGAAGGTGATG TATATACTTACATTAATGGAATATATAATATCTTTTTTTAAAAAAATGATGTTTAACAGCTGTTGGTATCATTGCCTAAATCAATTATATTATTAGTGTTGCAGAATGATGATACTCTAATTGTATCATTATTTTTT CATGTATTAACTCTGATACTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCCCCCAGGCTGCAGTGTAGTGGCGTGATCTCTGTTCACTGCAAGCTCCGCCTCTCGGGTTCACGCCATTCTCCTGCCTCAGCCTC CTGAGTAGCTGGGACTACAGGTGCCGGCCACCACGCCCGGCTAATTTTTTTGTATTTTTAGTAGCGACGGGGTTTCACCGTGTTAGCCAGGATGATCTCGATCTCCTGACCTCGTCATCCACCCGCCCTGGCCTCCC AAAGTGCTGGGATTACAGGCGTGAGCCACCACGCCCGGCCTATAACTTTGATACTTTTATAAAAGAAATTTACTCCTGATCAATTACTTTGCTTTCTGGAAGTCACTTTATCCAGGAAGGCCAAGATAAGTCCTTGT TTGTTTTCCTTTTTTGTCTATTTCCAAAATGGTAGTCCCCCACCTTATTCATGGTTTTGCTTTCTGTGGTTTCAGTTAAATGGAAAATTCCAGAAATAAATAGTTCATAAGTTTTACTTATTTATT 2

Know your method Can you tell when something has gone wrong? Can you determine why? 3

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Know your equipment Do you know how it works? Do you know how to fix it? 5

Know your procedure How do you get from point A to point B? 6

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Remember the assumptions EST’s: A snapshot of all detectable RNA’s [usually Poly(A)+] present in a give cell type, tissue, disease state, experimental condition or developmental stage. Know your technique Microarrays: A snapshot of all detectable RNA’s present in a given cell type, tissue, disease state, experimental conditions or How were the results/data developmental stage relative to a control. generated? What sources of error Proteomics: do these techniques produce? A snapshot of all detectable proteins in a given cell type, tissue, disease state, experimental condition or developmental stage cDNA Microarrays Microarrays Robotic microarrayer • cDNA microarrays • “GeneChip” in situ synthesized oligonucleotide arrays • Oligomer (~70mer) arrays 8

General Scanning ScanArray 3000 Chip Oligo Array Hybridization SEQUEST Database Search Mass Spectrometer Protein Database Nucleic Acid Database EST Database What about protein expression? Tandem Mass Spectrum Theoretical Mass Spectrum Correlation Analysis Ranked Score of Matched Peptides 9