A Structural Analysis of miRNA

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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_at_engr.smu.edu
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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

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

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TCGR Examples C Elegans miRNA
Window Size 5 Pattern Length 1
Pattern Length 2
A
C
G
U
AA
CC
GU
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TCGR Mature miRNA(Window5 Pattern1)
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TCGR Mature miRNA(Window5 Pattern2)
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TCGR Primate miRNA(Window9 Pattern1)



Ateles Geoffroyi Gorilla Gorilla
Homo Sapiens Lagothrix
Lagotricha
Lemur Catta Macaca Mulatta
Macaca Nemestrina Pan Paniscus
Pan Troglodytes Pongo Pygmaeus
Saguinus Labiatus
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TCGR Primate miRNA(Window9 Pattern2)



Ateles Geoffroyi Gorilla Gorilla
Homo Sapiens Lagothrix
Lagotricha
Lemur Catta Macaca Mulatta
Macaca Nemestrina Pan Paniscus
Pan Troglodytes Pongo Pygmaeus
Saguinus Labiatus
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TCGR Primate miRNA(Window9 Pattern3)



Ateles Geoffroyi Gorilla Gorilla
Homo Sapiens Lagothrix
Lagotricha
Lemur Catta Macaca Mulatta
Macaca Nemestrina Pan Paniscus
Pan Troglodytes Pongo Pygmaeus
Saguinus Labiatus
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TCGR Rodentia miRNA(Window9 Pattern123)
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TCGR Nematoda miRNA(Window9 Pattern123)
Caenorhabditis Briggsae Pattern1
Pattern2
Pattern3
Caenorhabditis Elegans Pattern1
Pattern2
Pattern3
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TCGR Viruses miRNA(Window9 Pattern123)
Epstein Barr Human Cytomegalovirus
Kaposi sarc Herpesvirus Mouse Gammaherpesvirus



Pattern1 Pattern2 Pattern3
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TCGR Rodent miRNA(Window9 Pattern123)



Ateles Geoffroyi Gorilla Gorilla
Homo Sapiens Lagothrix
Lagotricha
Lemur Catta Macaca Mulatta
Macaca Nemestrina Pan Paniscus
Pan Troglodytes Pongo Pygmaeus
Saguinus Labiatus
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TCGR Mature miRNA(Window5 Pattern3)
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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/
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TCGR Stem-Loops(Window5 Pattern1)
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TCGR Stem-Loops (Window5 Pattern2)
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TCGR Stem-Loops (Window5 Pattern3)
C Elegans
Homo Sapiens


Mus Musculus
All Mature