prognochip - base: an information system for the management of spotted dna microarray experiments

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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Management of Reporters Reporter Annotation Update





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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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Reporter Management Reporter Annotation Update





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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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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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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 !!!

prognochip - base: an information system for the management of spotted dna microarray experiments

Documents

analysis of microarray

data viewing

management of experimentswhat

comprehensive management

raw data sets reporters

microarray experimentation

gene ontology

main stepscreation