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PROGNOCHIP-BASE, FORTH-ICS
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PrognoChip-BASE: An Information System for the Management of
Spotted DNA MicroArray Experiments
Extension of BASE v 1.2.16 (Lund University)
Implementation: Haridimos Kondylakis, Dimitris Manakanatas, Manos Kalaitzakis
Guidance: Anastasia Analyti, Dimitris PlexousakisInstitute of Computer Science, FORTH-ICS, Crete, Greece
Department of Computer Science, University of Crete, Greece
Molecular Biologists: Dimitris Kafetzopoulos, Thanassis MargaritisInstitute of Molecular Biology & Biotechnology, FORTH-IMBB, Crete, Greece
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Spotted DNA Microarray Experiments
Normal Tissue RNAextraction Amplificatio
n
cy3labeling
Tumor Tissue RNAextraction
Amplification cy5 labeling
Hybridizationdata read out
Hybridization:mix RNAs and apply to array
Measure/Expression level
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Microarray Experiment Process
Plate
Array Fabrication
Plate Preparation
ArrayLabeled extract
extract
Samples
Labeling(protocol)
RNA extraction(protocol)
Images
Hybridized Array
Hybridization(protocol)
Scanning(protocol)
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Microarray Experiment Process (cont.)
Images
Channel 1 (cy3) Channel 2 (cy5)
Image Analysis
Raw Data
Spot Measures Spot Measures
Channel 1 (cy3) Channel 2 (cy5)
Normalization
Normalized data(relative expression levels)
Reporter Normalized value
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Microarray experimentation involves a massive amount of data for the biologist to organize and analyze:
Data to be stored before the experiment SamplesExtractsLabeled extractsReporters (oligonucleotides)Array DesignsArrays
Data to be stored after the experiment
HybridizationsImage filesRaw Data (measures from scanned images)Normalized data (relative expression levels)
Need for an Information System
(web-based)PrognoChip-
BASE
NormalizationPlug-ins
Submit/search/update
MIAME describes the minimum information that must be reported about microarray experiments, in order to be reproducible, and verifiable.
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BASE v1.2 at Lund University
• Web-based submission of data and queries
• Server: Linux, MySQL, php language, Apache web server, C++/Javascript
• Provides "plug-in"-able normalization, data viewing and analysis tools.
• Described in: 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.
• Available at: http://base.thep.lu.se/
BASE v1.2 (BioArray Software Environment) is an open source software package that manages all data related to microarrays (supports MIAME)
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PrognoChip-BASE is based on BASE v1.2.16, which was extended with additional functionality
Forms were modified to help the submitter and end user
Extra fields were added for describing extracts, labeled extracts, hybridizations, and raw data sets
Reporters were annotated with additional descriptors, external databases, and the Gene Ontology (GO)
Extra descriptors were added in the “List View” of main menu items
sorting, based on these descriptors, is provided
PrognoChip-BASE (FORTH-ICS)
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PrognoChip-BASE: Login
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PrognoChip-BASE: Main Steps
Creation and Management of MicroArrays Reporter Annotation Upload
Management of Reporters Reporter Annotation Update
Creation and Management of Biomaterials
Creation and Management of Hybridizations
Creation and Management of Experiments
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I1 I5I4I3I2 E4E3E2E1Gene structure
E2E1 E3 E4Transcriptome
Spliceome E1 E2 E3 E2 E4
5’ 3’
E3
Proteome
Protein 1 Protein 2
Transcript 1 Transcript 2
What is a Reporter
Reporter (oligonucleotide)
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Block Column Row Reporter Id Length Gene name Gene symbol Gene description
Block
Column
Row
Reporter: OligonucleotideDescription
Based on an array design,we producea batch of array slides
Array design
MicroArray Design
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List of Array Designs
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Creation of a New Array Design
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Reporter Map Upload
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Reporter Map Upload (cont.)
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Definition of a Reporter Map Format
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Creation of an Array Batch
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Creation of Array Batch and Array Slides
To each array batch corresponds a set of
array slides
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Creation of Array Slides
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PrognoChip-BASE: Main Steps
Creation and Management of MicroArrays Reporter Annotation Upload
Management of Reporters Reporter Annotation Update
Creation and Management of Biomaterials
Creation and Management of Hybridizations
Creation and Management of Experiments
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List of Reporters
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Gene Ontology (GO)
GO contains three different sub-ontologies/ taxonomies:
Molecular function
Biological process
Cellular component
Each term is related to its parent term through an is-a or part-of relationship
Unique identifier for every term:
GO:0003673(root=Gene Ontology)
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The Gene Ontology
Gene Ontology
Apoptotic protease activator
Apoptosis regulatorEnzyme activator
Apoptosis activator Protease activator
Molecular function Biological Process Cellular Component
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Gene Ontology Annotations
Evidence code GO annotations
The Biological Process, Molecular Function, and Cellular Component
GO Annotations should be given as semicolon (;) separated strings of the
following form:
GO_id | GO_name | evidence_code.
However, any part (i.e. "| evidence_code" ) is optional.
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Reporter Annotation Update
As in “Reporter Μap Upload”
Reporter Annotation Update
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Define a Reporter File Format
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Define a Reporter File Format (cont.)
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PrognoChip-BASE: Main Steps
Creation and Management of MicroArrays Reporter Annotation Upload
Reporter Management Reporter Annotation Update
Creation and Management of Biomaterials
Creation and Management of Hybridizations
Creation and Management of Experiments
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List of Samples
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Creation of a New Sample
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Creation of a New Extract
Extract quality indicators
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List of Labels
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Creation of a New Labeled Extract
Labeled extract quality indicators
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PrognoChip-BASE: Main Steps
Creation and Management of MicroArrays Reporter Annotation Upload
Reporter Management Reporter Annotation Update
Creation and Management of Biomaterials
Creation and Management of Hybridizations
Creation and Management of Experiments
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Creation of a Hybridization
Hybridization quality indicator
A hybridization is related with: • two or more labeled extracts• one array slide
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Creation of a Hybridization: Pick an Array Slide
Proceed with scanning
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Creation of a Scan
Every hybridization is associated with one or more scans• from different scanners
Optional: Upload of scanning images• Different image for each channel
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View of a Scan
Every scan is associated with one or more raw data sets• from different image analysis software
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Raw Data Set Upload
Continue as in
“Reporter Μap Upload”
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Raw Data Set Fields
PrognoChip-BASE additional raw data set
fields
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PrognoChip-BASE: Main Steps
Creation and Management of MicroArrays Reporter Annotation Upload
Reporter Management Reporter Annotation Update
Creation and Management of Biomaterials
Creation and Management of Hybridizations
Creation and Management of Experiments
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List of Experiments
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Creation of a New Experiment
If “study experiment” then it is verified that associated raw data sets correspond to the same cancerous and reference sample, but different array designs. Otherwise, a warning is displayed
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List of Raw Data Sets
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Assignment of Raw Data Sets to an Experiment
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General Information about an Experiment
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Creation of an Initial BioAssaySet
Creation of an initial BioAssaySet with the name PrognoChip
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Normalization Process
Exporting of results
Plug-in selection
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Plug-in Selection
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PrognoChip-BASE Web Site
http://www.ics.forth.gr/isl/projects/PrognoChip/
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Download PrognoChip-BASE
PrognoChip-BASE is released under the GNU General Public License
http://www.gnu.org/licenses/gpl.html
It can be downloaded from:
http://sourceforge.net/projects/prognochip-base/
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Acknowledgements
The development of PrognoChip-BASE was supported by National and EU funds within the contexts of:
the PrognoChip project (GSRT-EPAN) and the ACGT project (FP6-IST-026996).
PrognoChipPrognoChip
2004-2007 2006-2010
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Thank you !!!