Poster - DECIPHER Symposium 2009

1. An Interactive Genome Visualization
Tool Using DECIPHER Data
DECIPHER Symposium 2009
Rafael Jimenez (rafael@ebi.ac.uk) & Manuel Corpas (mc10@sanger.ac.uk)
Visualization tools have shown great potential in aiding
interpretation of genomic analysis. Using the DAS protocol,
integration of data has been used for visualization of different
sources of information on the same scale in genome browsers.
These usually offer a single view of the reference sequence with
different tracks and a chromosome on the top showing the section
viewed at one particular scale. In order to navigate through the
reference sequence refreshing is required, which may cause
significant delay in rendering of the page. This can be of great
detriment to the user experience, which may be accentuated if the
view requires massive amounts of data. DECIPHER, a web-based
database of genomic array data and phenotypes, relies heavily on
visualization tools for interpretation of copy number changes.
Currently DECIPHER uses two types of visualization involving 1)
Ensembl cytoview, which shows DECIPHER data as an integrated
track with other user-defined features and 2) its in-house built
Feature Graph, embedded in the patient report. Such tools allow
users to visually locate overlapping regions of interest and the ability
to refer back to the patient.
In terms of user usability, however, current visualization resources
offered in DECIPHER provide limited options in terms of views
showed and visualization of tracks. Moreover, the possibilities for
interactivity may be severely reduced due to the overhead in the
display data. KaryoDAS has been designed as a light-weight, user-
configurable solution for visualization of genomic information
sources using DAS technology. KaryoDAS makes genome
information readily visible in a full genomic context and offers
different views that interact with each other in a fast and intuitive
way. Here we use DECIPHER consented patient data and a
selection of sources as proof of principle for its enhanced user
interaction capabilities. We are able to show that KaryoDAS may
help researchers to navigate, compare annotations faster and
provide a more interactive interface than currently available genome
visualization tools, giving an overall enhanced visualization
experience for genome analysis results.
sources and displaying their content in a genomic context. The applicability of
DAS is also extended to protDASein sequence and structure data integrating
major protein databases like CATH, SCOP, MSD, InterPro, and Pfam. DAS
clients like SPICE and Dasty query DAS sources to display protein annotations
and related 3D structure and genome information.
DAS genome browsers are specialized to concentrate on derived features over
specific genome regions, in particular, gene structures and protein
sequences. However these systems are not designed for visually representing
features on a higher level of genome compaction. Interpretation of genome
information like copy number aberrations requires viewing the data in its full
genomic context. Thus, such genome browser do not employ an effective
exploratory visualization on a higher representation level.
As a solution we propose an exploratory information approach to integrate
genome information and make it readily visible in a manner that allows easy
interpretation of their full genomic context. We have developed a Karyotype
DAS client, a highly interactive web client to aid researchers to visualize,
share and compare annotations coming from DAS sources and genome
analysis DAS results. To aid researchers to include exploratory analysis and
tailored functional genomics results we are working on the next version of
GEPAS (The Gene Expression Profile Analysis Suite) to offer results in DAS
format. Moreover we have created a virtual DAS registry which allows
researchers with little knowledge about DAS to make their custom annotations
accessible in DAS format. Thus, researchers can integrate their annotations
and analysis results on our DAS client or any of the other DAS browsers.
Abstract
Implementation
As an example the Karyotype viewer includes a view of annotations from the
TCAG’s Database of Genomic Variants (DGV)—known as “the Toronto
Database” (turquoise blue), from a file of selected micro RNA (blue), from a
aCGH annotations (yellow) and from sequencing data (red). We selected the
former source from the DAS Registry while the other sources are made
available through the virtual DAS registry.
KaryotypeDASviewer
KaryoDAS
Service
broker
Service
consumer
Service
provider
Interact
PublishFind
Service Oriented Architecture
DAS
...
...
...
DAS
Registry
Ensembl
Reference
source
DECIPHER
Annotation
sources
KaryoDAS Protocol
KaryoDAS screenshot