Your SlideShare is downloading. ×
Show Me The Cp G Islands!
Upcoming SlideShare
Loading in...5
×

Thanks for flagging this SlideShare!

Oops! An error has occurred.

×
Saving this for later? Get the SlideShare app to save on your phone or tablet. Read anywhere, anytime – even offline.
Text the download link to your phone
Standard text messaging rates apply

Show Me The Cp G Islands!

384
views

Published on

Published in: Technology

0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total Views
384
On Slideshare
0
From Embeds
0
Number of Embeds
0
Actions
Shares
0
Downloads
6
Comments
0
Likes
0
Embeds 0
No embeds

Report content
Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
No notes for slide
  • Better title!! A Statistical Vacation to the CpG Islands in Summer 2005 New title! Show me the cpg islands (with statistical significance)
  • Transcript

    • 1. Show Me the CpG Islands!
      • Alicia Laughton (Mathematics ‘06)
      • Jessica Minnier (Mathematics ‘07)
      • Guided by Yung-Pin Chen (Mathematics/Statistics)
      (With Statistical Significance)
    • 2. This work is funded by John S. Rogers Science Research Program
    • 3. Outline
      • DNA Overview
      • CpG Islands
      • Methods
        • Traditional Method
        • Our Method
      • Future plans
    • 4. DNA
      • Deoxyribonucleic acid
      • Double-helix
      • Chain of nucleotide subunits
      • Contains genetic information
    • 5. Nucleotides
      • Made up of sugar, Phosphate, and bases
      • Four bases
        • Adenine (A)
        • Cytosine (C)
        • Guanine (G)
        • Thymine (T)
      • CpG represents a C directly followed by a G in the DNA sequence
    • 6. Methylation
      • Causes C to turn into T
      • Accounts for low occurrence of CpG dinucleotides in vertebrates
        • Expectation is 6.25% randomly
        • Actually 1% of total sequence (Bird 1986)
    • 7. Sequence AL031723
      • Human DNA sequence on chromosome 16
      • 3 known CpG Islands
      • Percentage of Content:
        • A - 22.7%
        • C - 29.5%
        • G - 28.3%
        • T - 19.5%
        • CpG - 3.1%
    • 8. CpG Islands
      • “ regions of DNA with a high G + C content and a high frequency of CpG dinucleotides relative to the bulk genome” -- Gardiner-Garden and Frommer (1987)
    • 9. CpG islands & Genes Gene 5’ end CpGi Gene Promoter CpG islands Gene CpG islands in body Gene 3’ end CpG islands
    • 10. What is important about CpG Islands?
      • Useful in identifying protein-coding regions (Yoon and Vaidyanathan, 2004)
        • Associated with “housekeeping genes” and 40% of tissue-specific genes
      • Aberrant methylation of CpG sites may cause silencing of tumor-suppressor genes (Deng, Zhou et al, 2002)
    • 11. aggcccgcccgcctagatcacttgaggtcacccgttcactcagtggctgacagcatcccctaaatcagcccttcaccaattattgacagtgtgtcctcaaccaaaagtagtcctccctgctccctccctcccctgatgtaattacatctcttcccatctttatttattttttgagacggagtcttgctctgtcacccaggctggagtgtagtggtgcaatctcggctcactgcacctctgcctcccgggttcaagcgattttcctgcctcagcccccggagtagctgggattacaggtgcccgccaccacacccagctaatttttgtatttttagtagagacggggtttcgccatgttggccaggctggtctcgaactcctgacctcaggtgatccgcctgcctcagcctcccaaagtgctgggattacagacgtgagccactgcggctggcctctctccccgtctttaactgtagccctgtgaattctcatcagcctgggcctggactcagcaggccaaaaagttaccagcagagcccagcacatgtgaggaaagtcggagacgtggcggcgccggccggaggatccttcccaagaccctgggccgctgtggccccctagatcttgcaggttgccagggtgccaggccagggagggggcctttctgagattctcctcattctgacacaggagaggagggcactgacccagtcccaaggtcccgggggaatcagccgaccacagcccaggactgtcccacctgggcagagagcccattctgggtgcccagcccgggcaggcccaggcacccccagcagtgccccgggcagcacctgccagccaggtagtgcagggtgaggttgggcagggcagggcgtggtaggtcagctgagcaaacagctcggagggagagctggggagggctgggaactaggtcgatagaaacacagggactgtgttagggaggggatgccttgccagtcacgcccagccctgactcctgccctctgagggggcttcccccacccctgctgacagccccaggaccggcccctgccaggaggctgacctgccaggagtgaccgccccagacttgagcccttgggaggcaggttctgagtccccttttcctgctcagacccccagggaaacgcaggctgggccagaggcagctgcacagacccctgcagtggggtgctcggtggagagcgctggaggtgggagggaggatgtgtgaggcagcgggagagaatccaggcttcccccacaacacccaccatgagcggtgcagagtaggggtgggcggcacgggagccttcccaccccgcagaaccaggccctgggcagagctggcctacagacgataccggacaagtcctcctccgtcttggtgacagagggagctgggactccctccacccacccactgccacttcagaagcagccacagggagactgggaggggcaggggtgctggggatgagcgtggggctcagccctccctcttcccaccctggagggctgcctccttccagcccacctggaagggtggtgtcagtcccagagcccctgcactccccgccccacctcctgcagctggaacccgcgtgggagccgcacccagcgtcccagggacaaacacagaggccttgggtggtggcggtaccaaggtctgaggcctggcagctcaggggcacccccgtccctgagagaggtcaagaaggggaggcaccaccccccaccacgggacctcgctgacgatgcccatagagagaaaccaggccagtgctgggaggggaaagaccccaggcctcatgagaagtcactgcctgcttttcccctcggccaggaaggaagccccaggcccttccctcccgtctcgggcatactgaccccaggcaccaagcgagaccaggagcccacccctttcctttcccagatggcacaccagtgactctgaatat cggagcgcacccctgctccctgggaggcaggatatcgtgccgctgctccctggggcgcacgataccctccccaggaaggcgccggtcagggcggacgggccagggtgctcaccggtaccaggcgaggccgcgctcgtagcacctgtcgaagaagtggggctcagagcccagcgcgcggacgtcggggtgcagccgcagaaactccagcagggcgcgcgtgccgcccttcttcacgccaacgatgagcgcttgcgggaagcgccggcggccgggaccgctggccaaaggcaggccgggtgctcccgggcggtggacggagctggacggctcggagggcgcgggggccggcgcgggggcgcgggcggccggcgggcagcggccggggagggcgcagaggcagtaggcgccgagcaccagggccacgagcagcatcggcgcgcgggacgcccgcagagcggccccttgcccggcccctgcgccctggccgcccccggccccgccgcccaggccgccgctacctgccatggggtcgcgccgctccaggcccgggagcgggggcagcaggcgggcgcgcatctcggcccgcgcgccgctcagtccgtgggtgcccggcttgtgctctgcgcccggcggtcccgcagcctgggagcgggcgcggggcgggaccgggggcggggtctggacgccctcccccctccccctcccccgcccactccgcctccgaggccactgcctgggctggacccgccggcagccgccaccacccgggcgcgactcgagctgccgggaccaccaggacgctcctgctccgagatcccaggccctggctcgcttgactccggcatcttcacctctgcgcggggaggatgcggcggcggtggccgttcgggacgcagggcagggacagggcggcgcgcgggcctcgggaccctctgtttgaagaccgatccccttccccccccaccccactccgggacgtgcgcggcaggtgcataggccaagccttggcctgcaggagcgggagcctcatcgccaggccaaggggacccaggaaaagcgtcgatccgggcactcggcctgccaagggagaaagaggccgggacagcaccctagtgtgcagagagggatcccagaacgtgtggggggagtctgcggccgggaatggcgtgcg cctcctcttcctgcctgctggagggaccagcaccaaaacaggaaagttcaccctgccaggccttctctccaaagagtcagagggagctccgtagggggatggggttcccggaccccctgccgtggaaggggagtgggaacacagacaggcggcaagggctttcgaggccccctcttgcacaaaccagctcagagatcggagatctttgggatcaattactttccctccccaggcatccgaagcctatcctagcccaggtgtggatgagggtgggagagacgggggaggagggagaggagcaggactggacccccgtgtgacaaacatctgacaagttgctctgaggactgcccccctccttgtggagcccacctcatctggtgtgcatttccctgcggctttcatccagccctgggcgaccctccctcctccatctcagcctccctcctcctgccccacacctcaggcctgggactcgcagatgccaaaagggcctggcagatgccaaagccagaaagtgcagggggactgcatcccccacaggagaccgggttcttccccactacatactcagaccccactccctgcacccactgctcttgcaaaccaggaactaaggggttcccctacccaccccgctccttgcctcctcttgcttttcttttgttttgtttgtttttgagacagagctgcactccagctgactcttgtcgcccaggctggagtgcagtggcacaatctcagctcactacaacctctgcctcccgggttcaagcgattctcctgcctcagcctcccaagtagctgggaatacaggcacccatcaccacgcctggctaatttttgtatttttagtagagatggggtttcaccatgttagtcaggctggtctcaaactcctgacctcaggtaatctgcccacctcagcctcccaaagggctgggattacaggcgtgagccactgtgccccaccctcctcttgcttttctaaaagatgatggtcaaagtacagcccccatttgcccccagacagggcacccttcccagatcgagaccttggggagtctgcgtgacccccacacctggcagacacaggtgcttcactagtgggggaacggctgagcatgtgctgagctcgggggcactagtgggctacagtccccaagtgggaggcccctcaagagcctggatgagctgactgacggtggagaggagggaaggagggcctatggccaaagtcaatccaggacccaactgccgaggccacaggaaggccgggtcaccgcctggaactaggtcggtcacagcccagtgggagccgtggcccggagactcaactgggggccctggttactctgctcgcctccccgcgtcggcacccagaacagagcttgcaggcactgggggcccagtccagggtctcaagagcagacaatgctgccttgcagttggggaaactgagacagggtgagaactttcagaggctcattgcaggctcctagcaggctgaaaggacggaggcacaggcacctaggagcacaccagccccacgtggccacggcccctcggagagcatgaggacacttgcaatgcggaagctcagcaggcccagctctactggctctgcaccgcccagtgaggggtcagcacagttggtccaagggacaataccagattaatgaggcagaagccacgggactgaccccttggaattctccacacccacactgtgcatccttaacccaaagcttctagcttggtagcccctcctaccctcctccctgcagcagggattagggatgcattctgacccctgcctgccgtcaggggagtgaggtctctccctggagcctgagctgaggatgcccaattcagccaggtgagccccgggatggactccatgtcccctagccaccacctgacttccccagcaccccacactggcaccagcccttcagatctcagaagcgagccaccctattctcacggagccccttcctgcctgccctccaaacccaagagtagttttagtacaaaaggcaaagttaacaaataggggtaggcgtcagggaaggaagaggatcagaggatcgggaacggagaaactggagcacctggagaagcgtctgggtcctgccacccccactgactccccaactggccttgggcagggtcctctctgcaggcgctgggtccaagcttggggatgagcagccaccagcgcgggctgcttcagctgaggctgccgcacccccacgtccatcctgggtagaggcaggacagccacagagccccatgcacggggctggactcaccctgggcactcacctaaaggcagtctcctcctttccaaagcccagactttctccggactcccaggaccaccaacaagggttcctgtgcgcagactcgggggtcttggggaggaaggacgctttctaggtggctgcctggaacctggaggcccctttctacagtacctggccagcggtcggtcacacctgagtgcccagagtgagcgggcggcagaggcatttctgacgctgccaggtaatcccacgggctggaaacgacctctgggctgggaagccaccgcctcccccagtcctgctgggtccctcagcagagagaacggaaccggggctttccccacagttttcaaagtttcagggaatcctagccaagtatcattccttcttccggagccgggaccccaggtcaagcctggggcccccacagggcggtcccaaccccactgcccggagcgcacccctgctccctgggaggcaggatatcgtgccgctgctccctggggcgcacgataccctccccaggaaggcgccggtcagggcggacgggccagggtgctcaccggtaccaggcgaggccgcgctcgtagcacctgtcgaagaagtggggctcagagcccagcgcgcggacgtcggggtgcagccgcagaaactccagcagggcgcgcgtgccgcccttcttcacgccaacgatgagcgcttgcgggaagcgccggcggccgggaccgctggcgtttccctcccaggggcccagtggtgaactgaattcaggcctgagacatactctgtctactaagtcaccccatctgcccagccttggtccacctggcactgcccagagacatcagtgatgcatttcggaagctggcaaagtggaccccactggagtacaaaggactcagggacccctgtgctggggaagagaaggagcccaggacctcccccaggggctgcctctgaggggcgtgagattcaggggcctctcgggtgggacctgcgggggccgctagacactgcgggaacttcacatccccaacgcccagcagcagcctgcagggaaggcaggggaggcgagccgggctcagagagggcgagcaacttgccccatccgaaggcaaaggtggtatgagacccgggtcctctctccacctctgccccagccttcctggccacagggctggcgccaggcaggcacggcacaggctcccggcagaggccacggtctcagccatccccacggtctcaggagtccccacggtctcagccgtccccacggtctgagtccccacggtctcagctgttcccacggtctcaggagtccccacaggttcagcagtccccacggtctcagccatccccacggtctcagccgtccccacagtctcagccatccccacggtctcagcagtccctactcaggacttgaaattccagcactggttccgtgatggctcctccagccccctgcccagcccagcatggtcatttccatctcctggcctttccgctgccgtctctctgctggatgctttatccttagtccccgctgagggcagaaggactttccaggaggaattgaccagaacgcagaacagcaggatgtggaatggactggggacagggagagagagatgcagggaccaggagtcggctcggagggttctcctggaagctgacccctccctccatcaggcactcggctgacggtggctacacacctcggggcgcccaggatggcagcactggggctgttcattcaccagtggatccccagcacctaacagagcctggcacgcagtggacattccattaatgtcgctcagtggaagggtatacgtgggaggagaggtcgggaaggctttctggaggtgacggccaggtgaagacgaggagaacagcattccaggccaaggaaccgtgtgggtgaaggctcagcagcagagagcccgggcagtagaggatggggtggagcttaaggccctgcgggaacaggggcggggcttagagtctggcctgaggctggtccagccccgcctcctcctcaggctcccaccaactctgagccaccagaccctcctttgtaaaatgaagacctcagtcatgactcgcatgagtctctgaagagtaacagctttattgtgatgtaattcacacaccactcaatccagccatttgtcgcatgcaaatcaatggttttcagtatattcatagtcgtgcaatcacaatcaattttagaacatttctatcaccccaaaaagaaatcctgtgtccattagcaatgacgccctcttctccccttcccacagcccctggcaaccacgaatctactttctgtctctatgggtttgcctattctggacatttcacaaaaagagaatcattgcttgaagccaggagttcaagaccaacctgggcaacaaagcgagaaccccgtctgtacaaaatattttaaatttagccaggcacagtggcgcacaccagtagtcccagcactttggaagtctgaggcaggaggttcacttgaggcggggaattcaaaaccagcctgggcaacatagggagtaccagtctctacaaaaaatttcaaaatttgccaagcgtgatggtatgcacctatagtcctagcttactcaggaggctgaggtgggaggatcgcttgagcccaggagtacgaggctgcagtgagccatgatcataccactgcattccagcctgggcgacagagtgagagcccatctctaaaacagaaagaaagaaagaaagaaatatggccagtcacagtggctcatgcctgtaatcccagcattttgggaggccaaggcaggtggatcacttgaggtcaggagttcgagaccagcctggccaacatggtgaaaccctgtctctaccaaaaatacataaattagccaggtgtgggccaggcgccatggcttacacttgtaatcccagcactttgggaggccgaggtgggcagatcacctgaggttgagagttcgagaccagcctgaccaacatgaagaaaccctgtctctactaaaaatacaaaaaattagctgggtgtggtggtgcatgcctgtaatctcagctacttgggaggctgaggaaggagaatggcttgaacccgggaggcagaggttgtggtgagccgagatcgcgcgattgcactccagcctgggcaacaacagcaaaactccatctcaaataataataataataaattagccaggtgtggtggtgcacgcctgtagtcccagctactcgggaggctgaggcacaagaaacccttgaacccgggaggcagaggttgcagtgaagctgaaattgcaccattccactccagcctgggagacagagtgagacaccatctctaaaatgaaaaaaaaaaaagagaatcatacaatgttcgtccttttgtgtctgggtctcttactcagcatgttctccaggttcatcaacactgtggcatgtgccagtacctccttcctcttcctgactgagtaatactccatcgtatggatggaccaccttttgttgattccctcattcgttgatggacatctaggttgtttccactgcggggttcttagtaacggtattacagggaaccatagattaccaggtatt How do you locate the CpG island in a DNA sequence?
    • 12.
      • agaattgcttgaaccgggaggcggaggttgcaatgagctgagatcacaccactgcactccagcatggtgacagagcaagactccatctcaaatcgagtaaaa aaaaaaaaatagctgggtgcggtggctcacgcctgtaatcccagcactttgggaggctgaggcgggtagatcacgaggtcaggagatcgtagccatcctggctaacacggtgaaaccccgtctctactaaaaatacaaaaagaaattagctgggcgtggtggtgggcgcctgtagtcccagctactcgggaggctgaggcaggagaatggcgtgaacccgggaggtggagcttgcagtgagtcgagatcacgccactgcactccagcctgggcgacagagcgagactcgatctcaaaaaaaaaaaaaaaaaaaaagtgcgacacgaggcacacagtcagtgcccagtggagttcgctgatatggttaccacatccctggggacagcgcctccaccctccaacctcgaggtttgtggaaaaatctgggtccaagctttatttcttaaatattcctctctgcccagcatgtgcacgcagcccgctctggccaggcgagcgggtgtcaatcaaggtgctgagcatccccagggtgccgctcagccccagccgaagtcctggcccgtcatctggtagaacctgcggttgaagggccggtagaactcctgcaggcgccggaccagggcctggggcacgcgtgggtgtggccggcccttggacttgcccaggcagcggggacggctgccgccctgggccttcttgaggcaggggaagcccttggtggcgttgaagtagaagtgcttgtccgtgacgacccgtttcaggcccaggaagtcctgcacgcggccgacctctccggccgggtcgctgaccagacgctccccgctgacgaacaggaagtgggacagggggaagtagcgcagccagtggtccaggtgctgggcgtacaggccgatgcggacggcgctccaggctgtgtccacggggcccaggccgtggcggaaggccagggcgcggaagctgggcaggcccggggtcttggagagcgtctgggcgtagtcggagatggcccgggtcacggggttccgcaccaccacgatcagcttcgtgtccggggacatggcgtggatgcggcggggggcctctcgcgtcacgaagtagctgggggtcttctccatggtgatctgcccatccagggttcggggcatcagactcctgcgggacgggtgcaaggagagggggcctgagcctccccagccctagaccggcccccaggggcccgggaccaaggcccccttatgcccgggaagcccaggcctccagggcgagcaagtcttcctccctgctcgggcccacccctgctagcgtgcgcggctgggcagcctggaacatggactgtgagggtgcccagcccggcacctgcctgcagcccggcctgttccgccggcctgccccgcctgctgctgcactgaggattagggtgacggtcgctggtcgggaggcccaaatgctcctcaccacccacatatcttccctgtgcaatccctgccgtcctcgcttccagagccagctccctcccaccggacccacactttcctggaactaggctgcccccagctcctttctcatcccagaccaagtaccccgaggcccgcccgcctagatcacttgaggtcacccgttcactcagtggctgacagcatcccctaaatcagcccttcaccaattattgacagtgtgtcctcaaccaaaagtagtcctccctgctccctccctcccctgatgtaattacatctcttcccatctttatttattttttg
      C+G Content: 0.492 Observed/Expected: 0.548
    • 13.
      • a gaattgcttgaaccgggaggcggaggttgcaatgagctgagatcacaccactgcactccagcatggtgacagagcaagactccatctcaaatcgagtaaaa aaaaaaaaatagctgggtgcggtggctcacgcctgtaatcccagcactttgggaggctgaggcgggtagatcacgaggtcaggagatcgtagccatcctggctaacacggtgaaaccccgtctctactaaaaatacaaaaagaaattagctgggcgtggtggtgggcgcctgtagtcccagctactcgggaggctgaggcaggagaatggcgtgaacccgggaggtggagcttgcagtgagtcgagatcacgccactgcactccagcctgggcgacagagcgagactcgatctcaaaaaaaaaaaaaaaaaaaaagtgcgacacgaggcacacagtcagtgcccagtggagttcgctgatatggttaccacatccctggggacagcgcctccaccctccaacctcgaggtttgtggaaaaatctgggtccaagctttatttcttaaatattcctctctgcccagcatgtgcacgcagcccgctctggccaggcgagcgggtgtcaatcaaggtgctgagcatccccagggtgccgctcagccccagccgaagtcctggcccgtcatctggtagaacctgcggttgaagggccggtagaactcctgcaggcgccggaccagggcctggggcacgcgtgggtgtggccggcccttggacttgcccaggcagcggggacggctgccgccctgggccttcttgaggcaggggaagcccttggtggcgttgaagtagaagtgcttgtccgtgacgacccgtttcaggcccaggaagtcctgcacgcggccgacctctccggccgggtcgctgaccagacgctccccgctgacgaacaggaagtgggacagggggaagtagcgcagccagtggtccaggtgctgggcgtacaggccgatgcggacggcgctccaggctgtgtccacggggcccaggccgtggcggaaggccagggcgcggaagctgggcaggcccggggtcttggagagcgtctgggcgtagtcggagatggcccgggtcacggggttccgcaccaccacgatcagcttcgtgtccggggacatggcgtggatgcggcggggggcctctcgcgtcacgaagtagctgggggtcttctccatggtgatctgcccatccagggttcggggcatcagactcctgcgggacgggtgcaaggagagggggcctgagcctccccagccctagaccggcccccaggggcccgggaccaaggcccccttatgcccgggaagcccaggcctccagggcgagcaagtcttcctccctgctcgggcccacccctgctagcgtgcgcggctgggcagcctggaacatggactgtgagggtgcccagcccggcacctgcctgcagcccggcctgttccgccggcctgccccgcctgctgctgcactgaggattagggtgacggtcgctggtcgggaggcccaaatgctcctcaccacccacatatcttccctgtgcaatccctgccgtcctcgcttccagagccagctccctcccaccggacccacactttcctggaactaggctgcccccagctcctttctcatcccagaccaagtaccccgaggcccgcccgcctagatcacttgaggtcacccgttcactcagtggctgacagcatcccctaaatcagcccttcaccaattattgacagtgtgtcctcaaccaaaagtagtcctccctgctccctccctcccctgatgtaattacatctcttcccatctttatttattttttg
      C+G Content: 0.501 Observed/Expected: 0.568
    • 14.
      • ag aattgcttgaaccgggaggcggaggttgcaatgagctgagatcacaccactgcactccagcatggtgacagagcaagactccatctcaaatcgagtaaaaa aaaaaaaatagctgggtgcggtggctcacgcctgtaatcccagcactttgggaggctgaggcgggtagatcacgaggtcaggagatcgtagccatcctggctaacacggtgaaaccccgtctctactaaaaatacaaaaagaaattagctgggcgtggtggtgggcgcctgtagtcccagctactcgggaggctgaggcaggagaatggcgtgaacccgggaggtggagcttgcagtgagtcgagatcacgccactgcactccagcctgggcgacagagcgagactcgatctcaaaaaaaaaaaaaaaaaaaaagtgcgacacgaggcacacagtcagtgcccagtggagttcgctgatatggttaccacatccctggggacagcgcctccaccctccaacctcgaggtttgtggaaaaatctgggtccaagctttatttcttaaatattcctctctgcccagcatgtgcacgcagcccgctctggccaggcgagcgggtgtcaatcaaggtgctgagcatccccagggtgccgctcagccccagccgaagtcctggcccgtcatctggtagaacctgcggttgaagggccggtagaactcctgcaggcgccggaccagggcctggggcacgcgtgggtgtggccggcccttggacttgcccaggcagcggggacggctgccgccctgggccttcttgaggcaggggaagcccttggtggcgttgaagtagaagtgcttgtccgtgacgacccgtttcaggcccaggaagtcctgcacgcggccgacctctccggccgggtcgctgaccagacgctccccgctgacgaacaggaagtgggacagggggaagtagcgcagccagtggtccaggtgctgggcgtacaggccgatgcggacggcgctccaggctgtgtccacggggcccaggccgtggcggaaggccagggcgcggaagctgggcaggcccggggtcttggagagcgtctgggcgtagtcggagatggcccgggtcacggggttccgcaccaccacgatcagcttcgtgtccggggacatggcgtggatgcggcggggggcctctcgcgtcacgaagtagctgggggtcttctccatggtgatctgcccatccagggttcggggcatcagactcctgcgggacgggtgcaaggagagggggcctgagcctccccagccctagaccggcccccaggggcccgggaccaaggcccccttatgcccgggaagcccaggcctccagggcgagcaagtcttcctccctgctcgggcccacccctgctagcgtgcgcggctgggcagcctggaacatggactgtgagggtgcccagcccggcacctgcctgcagcccggcctgttccgccggcctgccccgcctgctgctgcactgaggattagggtgacggtcgctggtcgggaggcccaaatgctcctcaccacccacatatcttccctgtgcaatccctgccgtcctcgcttccagagccagctccctcccaccggacccacactttcctggaactaggctgcccccagctcctttctcatcccagaccaagtaccccgaggcccgcccgcctagatcacttgaggtcacccgttcactcagtggctgacagcatcccctaaatcagcccttcaccaattattgacagtgtgtcctcaaccaaaagtagtcctccctgctccctccctcccctgatgtaattacatctcttcccatctttatttattttttg
      C+G Content: 0.500 Observed/Expected: 0.560
    • 15.
      • agaattgcttgaaccgggaggcggaggttg caatgagctgagatcacaccactgcactccagcatggtgacagagcaagactccatctcaaatcgagtaaaaaaaaaaaaatagctgggtgcggtggctcacgcctgtaatcccagcactttgggaggctgaggcgggtagatcacgaggtcaggagatcgtagccatcctggctaacacggtgaaaccccgtctctactaaaaatacaaaaagaaattagctgggcgtggtggtgggcgcctgtagtcccagctactcgggaggctgaggcaggagaatggc gtgaacccgggaggtggagcttgcagtgagtcgagatcacgccactgcactccagcctgggcgacagagcgagactcgatctcaaaaaaaaaaaa aaaaaaaaagtgcgacacgaggcacacagtcagtgcccagtggagttcgctgatatggttaccacatccctggggacagcgcctccaccctccaacctcgaggtttgtggaaaaatctgggtccaagctttatttcttaaatattcctctctgcccagcatgtgcacgcagcccgctctggccaggcgagcgggtgtcaatcaaggtgctgagcatccccagggtgccgctcagccccagccgaagtcctggcccgtcatctggtagaacctgcggttgaagggccggtagaactcctgcaggcgccggaccagggcctggggcacgcgtgggtgtggccggcccttggacttgcccaggcagcggggacggctgccgccctgggccttcttgaggcaggggaagcccttggtggcgttgaagtagaagtgcttgtccgtgacgacccgtttcaggcccaggaagtcctgcacgcggccgacctctccggccgggtcgctgaccagacgctccccgctgacgaacaggaagtgggacagggggaagtagcgcagccagtggtccaggtgctgggcgtacaggccgatgcggacggcgctccaggctgtgtccacggggcccaggccgtggcggaaggccagggcgcggaagctgggcaggcccggggtcttggagagcgtctgggcgtagtcggagatggcccgggtcacggggttccgcaccaccacgatcagcttcgtgtccggggacatggcgtggatgcggcggggggcctctcgcgtcacgaagtagctgggggtcttctccatggtgatctgcccatccagggttcggggcatcagactcctgcgggacgggtgcaaggagagggggcctgagcctccccagccctagaccggcccccaggggcccgggaccaaggcccccttatgcccgggaagcccaggcctccagggcgagcaagtcttcctccctgctcgggcccacccctgctagcgtgcgcggctgggcagcctggaacatggactgtgagggtgcccagcccggcacctgcctgcagcccggcctgttccgccggcctgccccgcctgctgctgcactgaggattagggtgacggtcgctggtcgggaggcccaaatgctcctcaccacccacatatcttccctgtgcaatccctgccgtcctcgcttccagagccagctccctcccaccggacccacactttcctggaactaggctgcccccagctcctttctcatcccagaccaagtaccccgaggcccgcccgcctagatcacttgaggtcacccgttcactcagtggctgacagcatcccctaaatcagcccttcaccaattattgacagtgtgtcctcaaccaaaagtagtcctccctgctccctccctcccctgatgtaattacatctcttcccatctttatttattttttg
      C+G Content: 0.712 Observed/Expected: 0.604 200 steps later…
    • 16.
      • agaattgcttgaaccgggaggcggaggttg caatgagctgagatcacaccactgcactccagcatggtgacagagcaagactccatctcaaatcgagtaaaaaaaaaaaaatagctgggtgcggtggctcacgcctgtaatcccagcactttgggaggctgaggcgggtagatcacgaggtcaggagatcgtagccatcctggctaacacggtgaaaccccgtctctactaaaaatacaaaaagaaattagctgggcgtggtggtgggcgcctgtagtcccagctactcgggaggctgaggcaggagaatggcgtgaacccgggaggtggagcttgcagtgagtcgagatcacgccactgcactccagcctgggcgacagagcgagactcgatctcaaa aaaaaaaaaaaaaaaaaagtgcgac acgaggcacacagtcagtgcccagtggagttcgctgatatggttaccacatccctggggacagcgcctccaccctccaacctcgaggtttgtggaaaaatctgggtccaagctttatttcttaaatattcctctctgcccagcatgtgcacgcagcccgctctggccaggcgagcgggtgtcaatcaaggtgctgagcatccccagggtgccgctcagccccagccgaagtcctggcccgtcatctggtagaacctgcggttgaagggccggtagaactcctgcaggcgccggaccagggcctggggcacgcgtgggtgtggccggcccttggacttgcccaggcagcggggacggctgccgccctgggccttcttgaggcaggggaagcccttggtggcgttgaagtagaagtgcttgtccgtgacgacccgtttcaggcccaggaagtcctgcacgcggccgacctctccggccgggtcgctgaccagacgctccccgctgacgaacaggaagtgggacagggggaagtagcgcagccagtggtccaggtgctgggcgtacaggccgatgcggacggcgctccaggctgtgtccacggggcccaggccgtggcggaaggccagggcgcggaagctgggcaggcccggggtcttggagagcgtctgggcgtagtcggagatggcccgggtcacggggttccgcaccaccacgatcagcttcgtgtccggggacatggcgtggatgcggcggggggcct ctcgc gtcacgaagtagctgggggtcttctccatggtgatctgcccatccagggttcggggcatcagactcctgcgggacgggtgcaaggagagggggc ctgagcctccccagccctagaccggcccccaggggcccgggaccaaggcccccttatgcccgggaagcccaggcctccagggcgagcaagtcttcctccctgctcgggcccacccctgctagcgtgcgcggctgggcagcctggaacatggactgtgagggtgcccagcccggcacctgcctgcagcccggcctgttccgccggcctgccccgcctgctgctgcactgaggattagggtgacggtcgctggtcgggaggcccaaatgctcctcaccacccacatatcttccctgtgcaatccctgccgtcctcgcttccagagccagctccctcccaccggacccacactttcctggaactaggctgcccccagctcctttctcatcccagaccaagtaccccgaggcccgcccgcctagatcacttgaggtcacccgttcactcagtggctgacagcatcccctaaatcagcccttcaccaattattgacagtgtgtcctcaaccaaaagtagtcctccctgctccctccctcccctgatgtaattacatctcttcccatctttatttattttttg
      C+G Content: 0.598 Observed/Expected: 0.421 600 steps later…
    • 17. Just a couple formulas…
      • G+C content =
        • (# of C’s) + (# of G’s )
        • length of window
      • Obs/Exp ratio =
        • Observed # of CpGs # of CpG’s in window
        • Expected # of CpGs (# of C’s)x(# of G’s)
        • length
      = From window
    • 18. Traditional Methods
      • Gardiner-Garden and Frommer (1987)
        • Window size 100 bp and Shift size 1bp
        • Criteria
          • At least 200 base pairs
          • G + C content greater than 50%
          • Expected portion of the Obs/Exp ratio calculated over the window
          • Obs/Exp ratio greater than 0.6
      • Takai and Jones (2002)
        • Window size 200 bp and Shift size 1bp
        • Criteria
          • At least 500 base pairs
          • At least 7 CpG dinucleotides in 200 base pair sequence
          • G + C content greater than 55%
          • Obs/Exp ratio calculated in same fashion as above method
          • Obs/Exp ratio greater than 0.65
    • 19. The Traditional Method C+G content Obs/Exp ratio C+G content /Obs-Exp ratio Base Position Sequence AL031723
    • 20.
      • Modifying the traditional methods
        • Window size 200 bp and Shift size 1 bp
        • Expected portion of the Obs/Exp ratio is based on whole sequence
      • And….
      Our Method
        • Observed # of CpGs # of CpG’s in window
        • Expected # of CpGs (# of C’s)x(# of G’s)
        • length
      = From entire sequence
    • 21.
      • Cutoffs greater than 97th percentile of observed sequence
      Obs/Exp Ratio G+C Content Mean: 0.0018 Standard Deviation: 0.0014 97th percentile: 0.0058 Mean: 0.5815 Standard Deviation: 0.0818 97th percentile: 0.7350 G+C Content Obs/Exp Ratio Number of Observations Number of Observations Sequence AL031723
    • 22. Kullback-Leibler Divergence
      • p ln (p/0.03) + (1-p) ln ((1-p)/(1-0.03))
      p KL Divergence
    • 23.
      • agaattgcttgaaccgggaggcggaggttgcaatgagctgagatcacaccactgcactccagcatggtgacagagcaagactccatctcaaatcgagtaaaaaaaaaaaaatagctgggtgcggtggctcacgcctgtaatcccagcactttgggaggctgaggcgggtagatcacgaggtcaggagatcgtagccatcctggctaacacggtga aaccccgtctctactaaaaatacaaaaagaaattagctgggcgtggtggtgggcgcctgtagtcccagctactcgggaggctgaggcaggagaatggcgtgaacccgggaggtggagcttgcagtgagtcgagatcacgccactgcactccagcctgggcgacagagcgagactcgatctcaaaaaaaaaaaaaaaaaaaaagtgcgacacgaggcacacagtcagtgcccagtggagttcgctgatatggttaccacatccctggggacagcgcctccaccctccaacctcgaggtttgtggaaaaatctgggtccaagctttatttcttaaatattcctctctgcccagcatgtgcacgcagcccgctctggccaggcgagcgggtgtcaatcaaggtgctgagcatccccagggtgccgctcagccccagccgaagtcctggcccgtcatctggtagaacctgcggttgaagggccggtagaactcctgcaggcgccggaccagggcctggggcacgcgtgggtgtggccggcccttggacttgcccaggcagcggggacggctgccgccctgggccttcttgaggcaggggaagcccttggtggcgttgaagtagaagtgcttgtccgtgacgacccgtttcaggcccaggaagtcctgcacgcggccgacctctccggccgggtcgctgaccagacgctccccgctgacgaacaggaagtgggacagggggaagtagcgcagccagtggtccaggtgctgggcgtacaggccgatgcggacggcgctccaggctgtgtccacggggcccaggccgtggcggaaggccagggcgcggaagctgggcaggcccggggtcttggagagcgtctgggcgtagtcggagatggcccgggtcacggggttccgcaccaccacgatcagcttcgtgtccggggacatggcgtggatgcggcggggggcctctcgcgtcacgaagtagctgggggtcttctccatggtgatctgcccatccagggttcggggcatcagactcctgcgggacgggtgcaaggagagggggcctgagcctccccagccctagaccggcccccaggggcccgggaccaaggcccccttatgcccgggaagcccaggcctccagggcgagcaagtcttcctccctgctcgggcccacccctgctagcgtgcgcggctgggcagcctggaacatggactgtgagggtgcccagcccggcacctgcctgcagcccggcctgttccgccggcctgccccgcctgctgctgcactgaggattagggtgacggtcgctggtcgggaggcccaaatgctcctcaccacccacatatcttccctgtgcaatccctgccgtcctcgcttccagagccagctccctcccaccggacccacactttcctggaactaggctgcccccagctcctttctcatcccagaccaagtaccccgaggcccgcccgcctagatcacttgaggtcacccgttcactcagtggctgacagcatcccctaaatcagcccttcaccaattattgacagtgtgtcctcaaccaaaagtagtcctccctgctccctccctcccctgatgtaattacatctcttcccatctttatttattttttg
      Kullback-Leibler: 0.508 Our Obs/Exp: 0.0029 C+G: 0.492
    • 24.
      • a gaattgcttgaaccgggaggcggaggttgcaatgagctgagatcacaccactgcactccagcatggtgacagagcaagactccatctcaaatcgagtaaaaaaaaaaaaatagctgggtgcggtggctcacgcctgtaatcccagcactttgggaggctgaggcgggtagatcacgaggtcaggagatcgtagccatcctggctaacacggtgaa accccgtctctactaaaaatacaaaaagaaattagctgggcgtggtggtgggcgcctgtagtcccagctactcgggaggctgaggcaggagaatggcgtgaacccgggaggtggagcttgcagtgagtcgagatcacgccactgcactccagcctgggcgacagagcgagactcgatctcaaaaaaaaaaaaaaaaaaaaagtgcgacacgaggcacacagtcagtgcccagtggagttcgctgatatggttaccacatccctggggacagcgcctccaccctccaacctcgaggtttgtggaaaaatctgggtccaagctttatttcttaaatattcctctctgcccagcatgtgcacgcagcccgctctggccaggcgagcgggtgtcaatcaaggtgctgagcatccccagggtgccgctcagccccagccgaagtcctggcccgtcatctggtagaacctgcggttgaagggccggtagaactcctgcaggcgccggaccagggcctggggcacgcgtgggtgtggccggcccttggacttgcccaggcagcggggacggctgccgccctgggccttcttgaggcaggggaagcccttggtggcgttgaagtagaagtgcttgtccgtgacgacccgtttcaggcccaggaagtcctgcacgcggccgacctctccggccgggtcgctgaccagacgctccccgctgacgaacaggaagtgggacagggggaagtagcgcagccagtggtccaggtgctgggcgtacaggccgatgcggacggcgctccaggctgtgtccacggggcccaggccgtggcggaaggccagggcgcggaagctgggcaggcccggggtcttggagagcgtctgggcgtagtcggagatggcccgggtcacggggttccgcaccaccacgatcagcttcgtgtccggggacatggcgtggatgcggcggggggcctctcgcgtcacgaagtagctgggggtcttctccatggtgatctgcccatccagggttcggggcatcagactcctgcgggacgggtgcaaggagagggggcctgagcctccccagccctagaccggcccccaggggcccgggaccaaggcccccttatgcccgggaagcccaggcctccagggcgagcaagtcttcctccctgctcgggcccacccctgctagcgtgcgcggctgggcagcctggaacatggactgtgagggtgcccagcccggcacctgcctgcagcccggcctgttccgccggcctgccccgcctgctgctgcactgaggattagggtgacggtcgctggtcgggaggcccaaatgctcctcaccacccacatatcttccctgtgcaatccctgccgtcctcgcttccagagccagctccctcccaccggacccacactttcctggaactaggctgcccccagctcctttctcatcccagaccaagtaccccgaggcccgcccgcctagatcacttgaggtcacccgttcactcagtggctgacagcatcccctaaatcagcccttcaccaattattgacagtgtgtcctcaaccaaaagtagtcctccctgctccctccctcccctgatgtaattacatctcttcccatctttatttattttttg
      Kullback-Leibler: 0.509 Our Obs/Exp: 0.0030 C+G: 0.501
    • 25.
      • ag aattgcttgaaccgggaggcggaggttgcaatgagctgagatcacaccactgcactccagcatggtgacagagcaagactccatctcaaatcgagtaaaaaaaaaaaaatagctgggtgcggtggctcacgcctgtaatcccagcactttgggaggctgaggcgggtagatcacgaggtcaggagatcgtagccatcctggctaacacggtgaaa ccccgtctctactaaaaatacaaaaagaaattagctgggcgtggtggtgggcgcctgtagtcccagctactcgggaggctgaggcaggagaatggcgtgaacccgggaggtggagcttgcagtgagtcgagatcacgccactgcactccagcctgggcgacagagcgagactcgatctcaaaaaaaaaaaaaaaaaaaaagtgcgacacgaggcacacagtcagtgcccagtggagttcgctgatatggttaccacatccctggggacagcgcctccaccctccaacctcgaggtttgtggaaaaatctgggtccaagctttatttcttaaatattcctctctgcccagcatgtgcacgcagcccgctctggccaggcgagcgggtgtcaatcaaggtgctgagcatccccagggtgccgctcagccccagccgaagtcctggcccgtcatctggtagaacctgcggttgaagggccggtagaactcctgcaggcgccggaccagggcctggggcacgcgtgggtgtggccggcccttggacttgcccaggcagcggggacggctgccgccctgggccttcttgaggcaggggaagcccttggtggcgttgaagtagaagtgcttgtccgtgacgacccgtttcaggcccaggaagtcctgcacgcggccgacctctccggccgggtcgctgaccagacgctccccgctgacgaacaggaagtgggacagggggaagtagcgcagccagtggtccaggtgctgggcgtacaggccgatgcggacggcgctccaggctgtgtccacggggcccaggccgtggcggaaggccagggcgcggaagctgggcaggcccggggtcttggagagcgtctgggcgtagtcggagatggcccgggtcacggggttccgcaccaccacgatcagcttcgtgtccggggacatggcgtggatgcggcggggggcctctcgcgtcacgaagtagctgggggtcttctccatggtgatctgcccatccagggttcggggcatcagactcctgcgggacgggtgcaaggagagggggcctgagcctccccagccctagaccggcccccaggggcccgggaccaaggcccccttatgcccgggaagcccaggcctccagggcgagcaagtcttcctccctgctcgggcccacccctgctagcgtgcgcggctgggcagcctggaacatggactgtgagggtgcccagcccggcacctgcctgcagcccggcctgttccgccggcctgccccgcctgctgctgcactgaggattagggtgacggtcgctggtcgggaggcccaaatgctcctcaccacccacatatcttccctgtgcaatccctgccgtcctcgcttccagagccagctccctcccaccggacccacactttcctggaactaggctgcccccagctcctttctcatcccagaccaagtaccccgaggcccgcccgcctagatcacttgaggtcacccgttcactcagtggctgacagcatcccctaaatcagcccttcaccaattattgacagtgtgtcctcaaccaaaagtagtcctccctgctccctccctcccctgatgtaattacatctcttcccatctttatttattttttg
      Kullback-Leibler: 0.507 Our Obs/Exp: 0.0029 C+G: 0.500
    • 26.
      • agaattgcttgaaccgggaggcggaggttgcaatgagctgagatcacaccactgcactccagcatggtgacagagcaagactccatctcaaatcgagtaaaaaaaaaaaaatagctgggtgcggtggctcacgcctgtaatcccagcacttt gggaggctgaggcgggtagatcacgaggtcaggagatcgtagccatcctggctaacacggtgaaaccccgtctctactaaaaatacaaaaagaaattagctgggcgtggtggtgggcgcctgtagtcccagctactcgggaggctgaggcaggagaatggc gtgaacccgggaggtggagcttgcagtgagtcgagatcacgccactgcactccagcctgggcgacagagcgagactcgatctcaaaaaaaaaaaaaaaaaaaaagtgcgacacgaggcacacagtcagtgcccagtggagttcgctgatatggttaccacatccctggggacagcgcctccaccctccaacctcgaggtttgtggaaaaatctgggtccaagc tttatttcttaaatattcctctctgcccagcatgtgcacgcagcccgctctggccaggcgagcgggtgtcaatcaaggtgctgagcatccccagggtgccgctcagccccagccgaagtcctggcccgtcatctggtagaacctgcggttgaagggccggtagaactcctgcaggcgccggaccagggcctggggcacgcgtgggtgtggccggcccttggacttgcccaggcagcggggacggctgccgccctgggccttcttgaggcaggggaagcccttggtggcgttgaagtagaagtgcttgtccgtgacgacccgtttcaggcccaggaagtcctgcacgcggccgacctctccggccgggtcgctgaccagacgctccccgctgacgaacaggaagtgggacagggggaagtagcgcagccagtggtccaggtgctgggcgtacaggccgatgcggacggcgctccaggctgtgtccacggggcccaggccgtggcggaaggccagggcgcggaagctgggcaggcccggggtcttggagagcgtctgggcgtagtcggagatggcccgggtcacggggttccgcaccaccacgatcagcttcgtgtccggggacatggcgtggatgcggcggggggcctctcgcgtcacgaagtagctgggggtcttctccatggtgatctgcccatccagggttcggggcatcagactcctgcgggacgggtgcaaggagagggggcctgagcctccccagccctagaccggcccccaggggcccgggaccaaggcccccttatgcccgggaagcccaggcctccagggcgagcaagtcttcctccctgctcgggcccacccctgctagcgtgcgcggctgggcagcctggaacatggactgtgagggtgcccagcccggcacctgcctgcagcccggcctgttccgccggcctgccccgcctgctgctgcactgaggattagggtgacggtcgctggtcgggaggcccaaatgctcctcaccacccacatatcttccctgtgcaatccctgccgtcctcgcttccagagccagctccctcccaccggacccacactttcctggaactaggctgcccccagctcctttctcatcccagaccaagtaccccgaggcccgcccgcctagatcacttgaggtcacccgttcactcagtggctgacagcatcccctaaatcagcccttcaccaattattgacagtgtgtcctcaaccaaaagtagtcctccctgctccctccctcccctgatgtaattacatctcttcccatctttatttattttttg
      200 steps later… Kullback-Leibler: 0.520 Our Obs/Exp: 0.0033 C+G: 0.712
    • 27.
      • agaattgcttgaaccgggaggcggaggttgcaatgagctgagatcacaccactgcactccagcatggtgacagagcaagactccatctcaaatcgagtaaaaaaaaaaaaatagctgggtgcggtggctcacgcctgtaatcccagcacttt gggaggctgaggcgggtagatcacgaggtcaggagatcgtagccatcctggctaacacggtgaaaccccgtctctactaaaaatacaaaaagaaattagctgggcgtggtggtgggcgcctgtagtcccagctactcgggaggctgaggcaggagaatggcgtgaacccgggaggtggagcttgcagtgagtcgagatcacgccactgcactccagcctgggcgacagagcgagactcgatctcaaaaaaaaaaaaaaaaaaaaagtgcgacacgaggcacacagtcagtgcccagtggagttcgctgatatggttaccacatccctggggacagcgcctccaccctccaacctcgaggtttgtggaaaaatctgggtccaagctttatttcttaaatattcctctctgcccagcatgtgcacgcagcccgctctggccaggcgagcgggtgtcaatcaaggtgctgagcatccccagggtgccgctcagccccagccgaagtcctggcccgtcatctggtagaacctgcggttgaagggccggtagaactcctgcaggcgccggaccagggcctggggcacgcgtgggtgtggccggcccttggacttgcccaggcagcggggacggctgccgccctgggccttcttgaggcaggggaagcccttggtggcgttgaagtagaagtgcttgtccgtgacgacccgtttcaggcccaggaagtcctgcacgcggccgacctctccggccgggtcgctgaccagacgctccccgctgacgaacaggaagtgggacagggggaagtagcgcagccagtggtccaggtgctgggcgtacaggccgatgcggacggcgctccaggctgtgtccacggggcccaggccgtggcggaaggccagggcgcggaagctgggcaggcccggggtcttggagagcgtctgggcgtagtcggagatggcccgggtcacggggttccgcaccaccacgatcagcttcgtgtccggggacatggcgtggatgcggcggggggcctct cgc gtcacgaagtagctgggggtcttctccatggtgatctgcccatccagggttcggggcatcagactcctgcgggacgggtgcaaggagagggggcctgagcctccccagccctagaccggcccccaggggcccgggaccaaggcccccttatgcccgggaagcccaggcctccagggcgagcaagtcttcctccctgctcgggcccacccctgctagcgtgcgcg gctgggcagcctggaacatggactgtgagggtgcccagcccggcacctgcctgcagcccggcctgttccgccggcctgccccgcctgctgctgcactgaggattagggtgacggtcgctggtcgggaggcccaaatgctcctcaccacccacatatcttccctgtgcaatccctgccgtcctcgcttccagagccagctccctcccaccggacccacactttcctggaactaggctgcccccagctcctttctcatcccagaccaagtaccccgaggcccgcccgcctagatcacttgaggtcacccgttcactcagtggctgacagcatcccctaaatcagcccttcaccaattattgacagtgtgtcctcaaccaaaagtagtcctccctgctccctccctcccctgatgtaattacatctcttcccatctttatttattttttg
      600 steps later… Kullback-Leibler: 0.510 Our Obs/Exp: 0.0030 C+G: 0.598
    • 28. Our Method KL Divergence*12 / Obs-Exp ratio*160 / C+G Content Base Position Kullback-Leibler Divergence Observed/Expected Ratio C+G Content Sequence AL031723
    • 29. Comparison of AL031723 Traditional Method Our Method
    • 30. Comparison of AL031723 Traditional Method Possible CpG Islands 3878-4534 5849-6136 6541-6820 8479-8698 10745-11049 18435-19580 25131-26359 35182-35441 36245-36576 36827-37606 Actual CpG Islands 18928-19547 25201-26371 36997-37693
    • 31. Comparison of AL031723 Our Method Possible CpG Islands 19227-19435 25197-26147 36982-37420 Actual CpG Islands 18928-19547 25201-26371 36997-37693
    • 32. Cons
      • Traditional Method
        • Criteria not stringent enough
        • If the expected part of the Obs/Exp ratio is unusually high then a high CpG count may not bring ratio above the cutoff
      • Our Method
        • Criteria sometimes too stringent
    • 33. Future Plans
      • CpG Islands
      • Linkage Disequilibrium and SNPs
        • Statistical analysis of the linkage disequilibrium coefficient
        • Kullback-Leibler Divergence II
    • 34. Thank you!
      • Former researchers
        • Andrew Dittmore
        • Yasuhiro Goda
        • Nick Heppenstall
        • Michal Dvir
      • Deborah Lycan
      • John S. Rogers Program