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Inf@Vis!

The digital magazine of InfoVis.net

Genome in a screen
by Juan C. Dürsteler [message nº 106]

The Human Genome Project (HGP) produces an intractable volume of information without using sophisticated means for its treatment. Information Visualisation has a lot to say in this field.
NCBI_Cromosoma.gif (23313 bytes)
NCBI (National Center for Biotechnology Information) entry point screen to the human genome database. You can see the 24 chromosomes. The user can click on a particular chromosome to browse the database or he/she can issue a direct query.
Screenshot by the author.
Click on the image to enlarge it.

HGP has a big potential to change our understanding of biology and to improve, for example, the possibilities to cure until now incurable diseases. 

Great emphasis (and some hype) has been put by the media on the giant leap that the complete sequentiation of the around 30,000 genes and around three billion bases present in the DNA helix of the human being means. The estimated date for the completion of the sequentiation is 2,005, although a “working draft” of it was published last spring. 

Genetics is a discipline where different forms of visualisation appeared very early, probably due to the fact that genes and the genome itself aren’t visible to the naked eye, so you have to imagine them. The DNA double helix is an elegant example of the visualisation of the geometry of a molecule (see for example the representation of DNA by Chemicalgraphics.com). 

The concept of “genetic map” was coined long ago. The 24 human chromosomes are displayed as “ideograms” that represent them in schematic form as rounded edged rectangles with a narrowed portion to indicate where the centromer is. (See the fogures)

An excellent starting point is the National Center for Biotechnology Information web site where you can find wide information , with databases about the human genome, that of several animals and links to other centers. In the “Tools” section you can find several analysis elements. One of them is MapViewer, a powerful Java applet that allows you to see and interactively query the graphical representation of the genes existing in the database. 

With Mapviewer you can interrogate the database in search of genes or markers against the whole genome or within a specific chromosome. The result is an ideogram of the chromosome with a lot of data about its genes. Clicking on the links associated to them you can get information about the known functions of the gene, the proteins it eventually codifies and a wide range of data, some of it quite exotic for the laymen (like me).

NCBI_Ideo.gif (44375 bytes)
MapViewer. Among other things Mapviewer allows you to see the ideogram of a particular chromosome. Just by clicking on the links to specific genes you can obtain a huge amount of information about many elements and features of the chromosome.
Screenshot by the author.
Click on the image to enlarge it

An old acquaintance of InfoVis.net, Ben Fry (do you remember Anemone, in issue number 67) from the Massachusetts Institute for Technology (MIT) is also working on genome visualisation. He has produced some innovative graphics, like the “Handheld Genome Browser” a genome browser to be used with handheld and PDA devices. Fry stands out by the clarity and elegance of his designs, as seen in another genome browser, reachable as a quicktime movie.

Once the genome is completed, the hardest work still lays ahead: to relate the expression of the genes with the features that make up the human being and that make it vulnerable to diseases like cancer or cystic fibrosis.

Working with such a huge amount of data makes it virtually indispensable to use visualisation, among other things, to identify patterns that repeat themselves in different organisms, and to approach the genome in a simple and affordable way.

Genome visualisation is a very specific field of visualisation, but it has a brilliant future, bound to a task of vast impact in the future of human beings.

Links of this issue:

http://www.chemicalgraphics.com/paul/images/DNA/Spotlight.jpg   Graphical representation of DNA by ChemicalGraphics.com.
http://www.ncbi.nlm.nih.gov/   National Center for Biotechnology Information (NCBI)
http://www.ncbi.nlm.nih.gov/Tools/index.html   Tools section on the web site del NCBI
http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/map_search?chr=hum_chr.inf&query   MapViewer
http://www.infovis.net/printMag.php?num=67&lang=2   Issue num. 67 with reference to Anemone, by Ben Fry
http://acg.media.mit.edu/people/fry/browser2/specifics.html   Handheld genome browser
http://acg.media.mit.edu/people/fry/gc/   Human genome visualisation tool by Ben Fry
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