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HilbertVis Visualisation of Genomic Data with Space-filling curves Simon Anders EMBL-EBI

HilbertVis Visualisation of Genomic Data with Space-filling curves Simon Anders EMBL-EBI. Visualizing genomic data Example: ChIP-Seq data from Barski et al. (Cell, 2007); histone methylation in the human genome Here: methylation patterns H3K4me1 and H3K4me3 on human chromosome 10.

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HilbertVis Visualisation of Genomic Data with Space-filling curves Simon Anders EMBL-EBI

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  1. HilbertVis Visualisation of Genomic Data with Space-filling curves Simon Anders EMBL-EBI

  2. Visualizing genomic data Example: ChIP-Seq data from Barski et al. (Cell, 2007); histone methylation in the human genome Here: methylation patterns H3K4me1 and H3K4me3 on human chromosome 10

  3. ChIP-Seq data and "pile-up" <-- Solexa reads, aligned to genome <-- "pile-up" vector Figure taken from Zhang et al., PLoS Comp. Biol. 2008

  4. Pile-up plot for chromosome 10 H3K4me1 H3K4me3

  5. Zoom-in H3K4me1 H3K4me3

  6. Hilbert curve, level 1

  7. Hilbert curve, level 2

  8. Hilbert curve, level 3

  9. Hilbert curve, level 4

  10. Hilbert plots of chromosome 10: H3K4me1 H3K4me3

  11. History The concept of space-filling curves is due to Giuseppe Peano (1890) This specific curve has been invented by David Hilbert (1891) The idea to use these curves for visualization was first published by Daniel Keim (1996) for economics data

  12. 3-color Hilbert plot red: H3K4me1 green: H3K4me3 blue: exons

  13. Graphical user interface

  14. Data handling R/Bioconductor package: Takes very-long R vectors Functions are supplied to help preparing these Stand-alone application: Can deal with GFF files and with wiggle track files (incl. BED files)

  15. Availability Open source, released under GPL v3 Bioconductor packaged "HilbertVis" and "HilbertVisGUI" http://www.ebi.ac.uk/~anders/hilbert/

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