1. A Structural Analysis of miRNA Margaret H. Dunham, Donya Quick, Yuhang Wang CSE Department Monnie McGee Jim Waddle Statistics Department Biology Department Southern Methodist University Dallas, Texas 75275 mhd@engr.smu.edu

2. Chaos Game Representation (CGR) 2D technique to visually see the distribution of subpatterns Our technique is based on the following: –Generate totals for each subpattern –Scale totals to a [0,1] range. (Note scaling can be a problem) –Convert range to red/blue 0-0.5: White to Blue 0.5-1: Blue to Red AC GU AC GU AC GU AC GU AC GU AC GU AC GU AC GU AC GU AC GU AC GU AC GU AC GU AC GU AC GU AC GU

3. CGR Example Homo Sapiens – all mature miRNA Patterns of length 3 UUC GUG

4. Temporal CGR (TCGR) Temporal version of Frequency CGR –In our context temporal means the starting location of a window 2D Array –Each Row represents counts for a particular window in sequence First row – first window Last row – last window We start successive windows at the next character location –Each Column represents the counts for the associated pattern in that window Initially we have assumed order of patterns is alphabetic –Size of TCGR depends on sequence length and subpattern lengt As sequence lengths vary, we only examine complete windows We only count patterns completely contained in each window.

5. TCGR Examples – C Elegans miRNA Window Size 5 Pattern Length 1 Pattern Length 2 Window 1 Positions 0-4 Window 2 Positions 1-5 Window 3 Positions 2-6 Window 13 Positions 12-16 Window 14 Positions 13-17 ACGU AACCGU

6. TCGR – Mature miRNA (Window=5; Pattern=1) All MatureMus Musculus Homo Sapiens C Elegans

7. TCGR – Mature miRNA (Window=5; Pattern=2) All MatureMus Musculus Homo SapiensC Elegans

8. TCGR – Primate miRNA (Window=9; Pattern=1) Ateles Geoffroyi Gorilla Gorilla Homo Sapiens Lagothrix Lagotricha Lemur Catta Macaca Mulatta Macaca Nemestrina Pan Paniscus Pan Troglodytes Pongo Pygmaeus Saguinus Labiatus

9. TCGR – Primate miRNA (Window=9; Pattern=2) Ateles Geoffroyi Gorilla Gorilla Homo Sapiens Lagothrix Lagotricha Lemur Catta Macaca Mulatta Macaca Nemestrina Pan Paniscus Pan Troglodytes Pongo Pygmaeus Saguinus Labiatus

10. TCGR – Primate miRNA (Window=9; Pattern=3) Ateles Geoffroyi Gorilla Gorilla Homo Sapiens Lagothrix Lagotricha Lemur Catta Macaca Mulatta Macaca Nemestrina Pan Paniscus Pan Troglodytes Pongo Pygmaeus Saguinus Labiatus

11. TCGR – Rodentia miRNA (Window=9; Pattern=1;2;3) Mus Musculus Pattern=1 Pattern=2 Pattern=3 Rattus Norvegicus Pattern=1 Pattern=2 Pattern=3

12. TCGR – Nematoda miRNA (Window=9; Pattern=1;2;3) Caenorhabditis Briggsae Pattern=1 Pattern=2 Pattern=3 Caenorhabditis Elegans Pattern=1 Pattern=2 Pattern=3

13. TCGR – Viruses miRNA (Window=9; Pattern=1;2;3) Epstein Barr Human Cytomegalovirus Kaposi sarc Herpesvirus Mouse Gammaherpesvirus Pattern =1 Pattern =2 Pattern =3

14. TCGR – Rodent miRNA (Window=9; Pattern=1;2;3) Ateles Geoffroyi Gorilla Gorilla Homo Sapiens Lagothrix Lagotricha Lemur Catta Macaca Mulatta Macaca Nemestrina Pan Paniscus Pan Troglodytes Pongo Pygmaeus Saguinus Labiatus

15. TCGR – Mature miRNA (Window=5; Pattern=3) All Mature Mus Musculus Homo Sapiens C Elegans ACG CGCGCGUCG

16. Stem-Loop miRNA Datasets Supersequence of pre-miRNA: “ … not strictly precursor miRNAs (pre-miRNAs), but include the pre-miRNA and some flanking sequence from the presumed primary transcript. “ (microrna.sanger.ac.uk)microrna.sanger.ac.uk Mus Musculus –270 sequences –Maximum length 128 –Minimum length 61 Caenorhabditis Elegans –114 sequences –Maximum length 115 –Minimum length 72 Homo Sapiens –332 sequence –Maximum length 137 –Minimum length 58 All mature –3518 sequences –Maximum length 509 –Minimum length 58 Source: miRBase (Release 8.0; 4/3/06) http://microrna.sanger.ac.uk/sequences/

17. TCGR – Stem-Loops (Window=5; Pattern=1) All MatureMus Musculus Homo Sapiens C Elegans

18. TCGR – Stem-Loops (Window=5; Pattern=2) All MatureMus Musculus Homo SapiensC Elegans

19. TCGR – Stem-Loops (Window=5; Pattern=3) C ElegansHomo Sapiens Mus MusculusAll Mature