|
The Genomic Information
System (Genomic IS) of PrognoChip,
called PrognoChip-BASE, is based on the BioArray Software Environment
(BASE v1.2.16) [1].
BASE v1.2 is a MIAME-compliant database and analysis platform,
designed to be installed
in any microarray laboratory and serve many users simultaneously via the web. BASE v1.2 was developed by
Lund University and is a free software release, under the GNU General Public License. It runs on a Linux
Server, using a MySQL database backend.
In short, BASE v1.2 manages
biomaterials (samples, extracts, labeled extracts), reporters/genes and related annotations, as well
as array production and hybridizations. When all related information is available, raw hybridization
data (called measured bioassay data in
MAGE-OM: MicroArray and Gene
Expression - Object Model)
can be stored. Several scanners and image processors are supported. Each step of a microarray
experiment is associated with a protocol description. Raw hybridization data
can be organized in Experiments and normalized.
Normalization plug-ins are already installed in BASE v1.2, but it is also possible to develop and install
your own
plug-ins. Normalization is performed in a hierarchical way and several normalization methods (such as, lowess,
median) can be performed to refine intermediate results.
PrognoChip-BASE extends BASE v1.2.16, in order to ease biologist’s task
and to provide more functionalities. In particular,
several quality indicators have been added to
Extracts, Labeled Extracts, and Hybridizations to provide users
with the capability of storing and reviewing the quality of their experiments.
Further,
new raw hybridization data fields have been added. Additionally, reporter annotations have been extended with
(i) the type of the reporter, (ii) the number of transcripts of the corresponding gene ,
(iii) the description of the corresponding protein, (iv) the location of the reporter, and (v)
ids to additional public databases,
such as Ensembl and
EMBL. Reporters are further annotated with
Gene Ontology (GO)
ids/names/evidence code. List views of menu items are enhanced
with additional descriptors and sorting on these descriptors is provided.
In PrognoChip-BASE, experiments participating
in PrognoChip studies are called study experiments and are marked with a special flag.
For these experiments, an integrity constraint verifies that the same (cancerous and “reference”)
samples are used in all participating hybridizations and that the designs of the participating arrays are
different. This guarantees that a study experiment in PrognoChip-BASE corresponds to a single wet
lab experiment, where multiple array slides (with different array designs) are used to cover
the whole human genome.
The Genomic IS of PrognoChip has been installed in the participating molecular biology lab at FORTH-IMBB.
[1] L. H. Saal, C. Troein, J. Vallon-Christersson, S. Gruvberger, A. Borg,
and C. Peterson, BioArray Software Environment: A Platform for Comprehensive Management and Analysis of
Microarray Data, Genome Biology, 3(8): software0003.1-0003.6, 2002.
Overview: pdf
Presentation: ppt
PrognoChip-BASE is released under the GNU General Public License and
it can be downloaded
from SourceForge.net. Details about the installation can be found
in the Documentation folder of the package.
|
Genomic IS 
