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A Structural Analysis of miRNA

A Structural Analysis of miRNA

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A Structural Analysis of miRNA

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  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. A A A A A A A A A A A A A A A A C C C C C C C C C C C C C C C C G G G G G G G G G G G G G G G G U U U U U U U U U U U U U U U U 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

  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. 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 TCGR Examples – C Elegans miRNA Window Size 5 Pattern Length 1 Pattern Length 2 A C G U AA CC GU

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

  7. C Elegans Homo Sapiens Mus Musculus All Mature TCGR – Mature miRNA(Window=5; Pattern=2)

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

  12. TCGR – Nematoda miRNA(Window=9; Pattern=1;2;3) Caenorhabditis BriggsaePattern=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. C Elegans Homo Sapiens Mus Musculus All Mature ACG CGC GCG UCG TCGR – Mature miRNA(Window=5; Pattern=3)

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

  18. C Elegans Homo Sapiens Mus Musculus All Mature TCGR – Stem-Loops (Window=5; Pattern=2)

  19. TCGR – Stem-Loops (Window=5; Pattern=3) C Elegans Homo Sapiens Mus Musculus All Mature