Visualisation for Functional Genomics and Drug Target Discovery

1
Visualisation for Functional Genomics and Drug
Target Discovery

• Asia Jakubowska
• Department of Computing Science
• University of Glasgow
• http//www.dcs.gla.ac.uk/asia

2
Motivation

• Growing amounts of biological data (typically
  millions of objects on a chromosome)
• Cognitive problem how to understand the data
• How to compare data coming from various sources
  and experiments
• Solution visualisation

3
User activity search for genes responsible for
hypertension

• µArray experiments (analysing the activity of
  genes, including faulty genes)
• hypertension
• rat breeding interpretation MAP

4
Research Goals

• Develop new visualisation techniques
• Compare existing genome visualisation browsers
• Solve some visualisation and data integration
  problems
• Build a new visualisation tool (VisGenome)
• Prove that it is better than other tools
• Explain why it is better

5
Genome browser

• Chromosome 100-290 mln letters
• QTL chromosomal region associated with a
  disease
• QTL 3-50 mln letters
• Gene 20-70 kb letters
• Microarray probe 25 letters
• SNP (Single Nucleotide Polymorphism) 1 letter

6
New genome browsers classification

• A classification according to three dimensions
• genome browsers represent between one and many
  species,
• the size of the objects shown,
• complexity linear and graph representation.

7
New genomebrowsersclassification
8
Ensembl browser

• An interactive Web site, a set of flat files, and
  a complete, portable open source software system
  for handling genomes
• Genome browser in SyntenyView
• Clickable picture

9
Ensembl browser

• ContigView, MultiContigView
• Labelling and searching

10
SyntenyVista

• Information about the human, rat and mouse
  genomes
• Relationships between chromosomes

11
SyntenyVista

• Smooth zooming and panning
• Colours, searching, top panel
• Manipulate the view
• Database connection

12
BugView

• Genome browser
• Information provided by the files
• Navigation of a genome by scrolling and smoothly
  zooming
• Moving the views with the data

13
DerBrowser

• Visualisation and presentation molecular genetic
  and associated data
• Database connection and data from file
• Scrolling, zooming, searching

14
Artemis

• Sequence viewer and annotation tool
• Artemis provides two sequence windows to view
  the same sequence at different levels
  simultaneously

15
Apollo

• Genome viewer and editor
• Comparison between two species Drosophilla
  pseudoobscura and Diosophila melanogaster
• Allows to explore genomic annotations at many
  levels of detail
• Possible context-dependent menu, zooming and
  semantic zooming

16
Sockeye

• 3D graphic technology project
• Simultaneously visualise several different
  alignments and easily view their underlying gaps
• 3D viewport
• Zooming, panning and rotating the position of the
  sequence track
• Easily customize the users own installation
• There are no labels

17
Software development of DerBrowser exploration
of QTL presentation
18
DerBrowser investigation of comparative genome
display

• A comparison for rat, mouse and human chromosomes
• Impossible to move the chromosomes to see the
  comparisons

19
DerBrowser selection of a chromosome fragment
via CGI script

• The solution allows for choosing the coordinates
  to display only a specified part of the chromosome

20
VisGenome

• View A shows chromosomes from three species in
  the upper part of the display and the chromosomes
  for which data has been received from Ensembl in
  the lower part.
• View B contains an overview and detail for the
  rat chromosome 18.

21
Future experimental work

• tests with the hypertension and schizophrenia
  biological research groups
• questions about visualisation techniques and
  their usability during biological work
• measuring the time during the experiment
• counting the mouse clicks
• recording the experiments for future analysis
• release VisGenome

22
Summary

• Review of genomic browsers
• Work done
• Future directions
• Questions?