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 [email protected] A. A. A. A. A. A. A. A. A. A. A. A. A.

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A Structural Analysis of miRNA

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A structural analysis of mirna

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

[email protected]


Chaos game representation cgr

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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


Cgr example

CGR Example

Homo Sapiens – all mature miRNA

Patterns of length 3

UUC

GUG


Temporal cgr tcgr

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.


Tcgr examples c elegans mirna

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


Tcgr mature mirna window 5 pattern 1

C Elegans

Homo Sapiens

Mus Musculus

All Mature

TCGR – Mature miRNA(Window=5; Pattern=1)


Tcgr mature mirna window 5 pattern 2

C Elegans

Homo Sapiens

Mus Musculus

All Mature

TCGR – Mature miRNA(Window=5; Pattern=2)


Tcgr primate mirna window 9 pattern 1

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


Tcgr primate mirna window 9 pattern 2

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


Tcgr primate mirna window 9 pattern 3

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


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

TCGR – Rodentia miRNA(Window=9; Pattern=1;2;3)


Tcgr nematoda mirna window 9 pattern 1 2 3

TCGR – Nematoda miRNA(Window=9; Pattern=1;2;3)

Caenorhabditis BriggsaePattern=1 Pattern=2 Pattern=3

Caenorhabditis Elegans Pattern=1 Pattern=2 Pattern=3


Tcgr viruses mirna window 9 pattern 1 2 3

TCGR – Viruses miRNA(Window=9; Pattern=1;2;3)

Epstein Barr Human Cytomegalovirus Kaposi sarc Herpesvirus Mouse Gammaherpesvirus

Pattern=1

Pattern=2

Pattern=3


Tcgr rodent mirna window 9 pattern 1 2 3

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


Tcgr mature mirna window 5 pattern 3

C Elegans

Homo Sapiens

Mus Musculus

All Mature

ACG

CGC

GCG

UCG

TCGR – Mature miRNA(Window=5; Pattern=3)


Stem loop mirna datasets

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/


Tcgr stem loops window 5 pattern 1

C Elegans

Homo Sapiens

Mus Musculus

All Mature

TCGR – Stem-Loops(Window=5; Pattern=1)


Tcgr stem loops window 5 pattern 2

C Elegans

Homo Sapiens

Mus Musculus

All Mature

TCGR – Stem-Loops (Window=5; Pattern=2)


Tcgr stem loops window 5 pattern 3

TCGR – Stem-Loops (Window=5; Pattern=3)

C Elegans

Homo Sapiens

Mus Musculus

All Mature


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