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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@engr.smu.edu. A. A. A. A. A. A. A. A. A. A. A. A. A.

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slide1

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

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