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German Russian Workshop 2011 - geneXplain
1. Towards a comprehensive
computational platform for next
generation drug development –
A Russian‐German joint venture
Edgar Wingender
CEO
Wolfenbüttel, Am Exer 10b
GmbH http://www.genexplain.com
2. We aim to provide a comprehensive platform of
bioinformatics, systems biological and cheminformatics
tools for a
personalized medicine and pharmacogenomics
3. Some facts about geneXplain:
Founded in April 2010, starting active business July 2010
International (German-Russian) shareholder structure
Managing directors: E. Wingender (CEO), A. Kel (CSO)
Product portfolio in bioinformatics, systems biology,
cheminformatics
Development close to science and research
Participation in international and national research consortia
- SYSCOL (EU FP7)
- GERONTOSHIELDS (BMBF)
5. Some facts about geneXplain:
Founded in April 2010, starting active business July 2010
International (German-Russian) shareholder structure
Managing directors: E. Wingender (CEO), A. Kel (CSO)
Product portfolio in bioinformatics, systems biology,
cheminformatics
Close to science and research
Participation in international and national research
consortia
- SYSCOL (EU FP7)
- GERONTOSHIELDS (BMBF)
- TEMPUS (EU)
6. The idea:
Providing a platform of methods for
Biomedical research
Focus: drug development
Complete pipeline from high-throughput data to a lead structure
High-throughput data:
Genomics
Transkriptomics
Proteomics
Public private partnership
7. GeneXplainTM Platform: A Workflow for Drug Discovery
The geneXplain platformTM is a new product integrating bio- and cheminformatics tools for pharmacogenomics.
It provides a drug discovery workflow that guides from the statistical analysis of biological high-throughput
data to a panel of potential lead compounds for further validation.
Statistics
Input: High-throughput data
from patients (genomics,
Within the geneXplain platformTM,
transcriptomics, ChIP-seq,
identification of drug target protein
proteomics, etc.)
molecules by bioinformatics and
Output: List of relevant genes or
systems biology methods, is
proteins
complemented by prediction of
Any pre-processed list of biological activities and adverse
genes or proteins from
Bioinformatics effects for chemical compounds,
own experiments, from
Search for regulatory modules in any literature or databases based on multilevel neighborhoods
genomic regions of atoms (MNA) descriptors.
Output: List of transcription factors
potentially responsible for the observed
(co-)regulation of genes
Any list of transcription factors;
any list of genes or proteins from
own experiments, from literature
Systems Biology
The workflow or databases to be mapped on
Topological analysis of the networks known pathways
The incorporated statistical upstream of transcription factors,
analyses help to identify relevant simulation of the network behavior,
genes or proteins in the raw patient stratification
data, e.g. those that are Hypotheses about
gene regulators Output: List of potential master regulators
differentially expressed.
essential for the
The Bioinformatics block allows
studied process
to reveal potential regulation of
genes by transcription factors or
miRNAs.
Systems biology approaches
analyze networks of molecular Cheminformatics
events and suggest promising Prediction of biological activities of the
Hypotheses compounds, selection of compounds with
drug target molecules and their about target
mechanisms of action. required effects and without adverse or
molecules and
The integrated PASS tool enables their role in the toxic effects.
to direct compound screening by studied process Output: List of potential lead structures
pre-selection of chemicals with Hypotheses for for validation
desirable and without adverse or validations and clinical
toxic effects. trials
Systematic generation of
statistically significant
hypotheses
8. Proof of concept: Net2Drug consortium
EU FP6, Coordinator: A. Kel
Transcriptomics breast cancer cell line
Statistical evaluation
Integrated bioinformatic analysis
(promoter & pathway analysis)
Systems biological simulation
Cheminformatic identification of candidate drugs
9. Proof of concept: Net2Drug consortium
EU FP6, Coordinator: A. Kel
Transcriptomics breast cancer cell line
Results: Statistical evaluation
Out of 24 million compounds, 16 substances turned out
to be feasibleIntegrated bioinformatic analysis
for experimental testing.
(promoter & pathway analysis)
For 2 compounds, highly specific activities were found.
Systems biological simulation
Cheminformatic identification of candidate drugs
10. GeneXplainTM Platform: A Workflow for Drug Discovery
The geneXplain platformTM is a new product integrating bio- and cheminformatics tools for pharmacogenomics.
It provides a drug discovery workflow that guides from the statistical analysis of biological high-throughput
data to a panel of potential lead compounds for further validation.
Statistics
Input: High-throughput data
from patients (genomics,
Within the geneXplain platformTM,
transcriptomics, ChIP-seq,
identification of drug target protein
proteomics, etc.)
molecules by bioinformatics and
Output: List of relevant genes or
systems biology methods, is
proteins
complemented by prediction of
Any pre-processed list of biological activities and adverse
genes or proteins from
Bioinformatics effects for chemical compounds,
own experiments, from
Search for regulatory modules in any literature or databases based on multilevel neighborhoods
genomic regions of atoms (MNA) descriptors.
Output: List of transcription factors
potentially responsible for the observed
(co-)regulation of genes
Any list of transcription factors;
any list of genes or proteins from
own experiments, from literature
Systems Biology
The workflow or databases to be mapped on
Topological analysis of the networks known pathways
The incorporated statistical upstream of transcription factors,
analyses help to identify relevant simulation of the network behavior,
genes or proteins in the raw patient stratification
data, e.g. those that are Hypotheses about
gene regulators Output: List of potential master regulators
differentially expressed.
essential for the
The Bioinformatics block allows
studied process
to reveal potential regulation of
genes by transcription factors or
miRNAs.
Systems biology approaches
analyze networks of molecular Cheminformatics
events and suggest promising Prediction of biological activities of the
Hypotheses compounds, selection of compounds with
drug target molecules and their about target
mechanisms of action. required effects and without adverse or
molecules and
The integrated PASS tool enables their role in the toxic effects.
to direct compound screening by studied process Output: List of potential lead structures
pre-selection of chemicals with Hypotheses for for validation
desirable and without adverse or validations and clinical
toxic effects. trials
Systematic generation of
statistically significant
hypotheses
11. The cheminformatics portfolio:
PASS
predicts biological activities of chemical compounds from their structural formulae; assigns
probability values to each activity and identifies those parts of the molecule that are responsible
for this activitiy
PharmaExpert
mines large amounts of predictions generated by PASS to filter out those compounds that
optimaly fit user-defined requirements
GUSAR
generates quantitative structure-activity relationship (QSAR) models
12. How to get there:
GeneXplainTM Platform: A Workflow for Drug Discovery
The geneXplain platformTM is a new product integrating bio- and cheminformatics tools for pharmacogenomics.
It provides a drug discovery workflow that guides from the statistical analysis of biological high-throughput
data to a panel of potential lead compounds for further validation.
Statistics
Input: High-throughput data
from patients (genomics,
Within the geneXplain platformTM,
transcriptomics, ChIP-seq,
identification of drug target protein
proteomics, etc.)
molecules by bioinformatics and
Output: List of relevant genes or
systems biology methods, is
proteins
complemented by prediction of
Any pre-processed list of biological activities and adverse
genes or proteins from
Bioinformatics effects for chemical compounds,
own experiments, from
Search for regulatory modules in any literature or databases based on multilevel neighborhoods
genomic regions of atoms (MNA) descriptors.
Output: List of transcription factors
potentially responsible for the observed
(co-)regulation of genes
Any list of transcription factors;
any list of genes or proteins from
own experiments, from literature
Systems Biology
The workflow or databases to be mapped on
Topological analysis of the networks known pathways
The incorporated statistical upstream of transcription factors,
analyses help to identify relevant simulation of the network behavior,
genes or proteins in the raw patient stratification
data, e.g. those that are Hypotheses about
gene regulators Output: List of potential master regulators
differentially expressed.
essential for the
The Bioinformatics block allows
studied process
to reveal potential regulation of
genes by transcription factors or
miRNAs.
Systems biology approaches
analyze networks of molecular Cheminformatics
events and suggest promising Prediction of biological activities of the
Hypotheses compounds, selection of compounds with
drug target molecules and their about target
mechanisms of action. required effects and without adverse or
molecules and
The integrated PASS tool enables their role in the toxic effects.
to direct compound screening by studied process Output: List of potential lead structures
pre-selection of chemicals with Hypotheses for for validation
desirable and without adverse or validations and clinical
toxic effects. trials
Systematic generation of
statistically significant
hypotheses
13. The way:
The geneXplain platform
Integrated collection of bioinformatic and systems
biological program modules („Bricks“)
Based on proven BioUML technology
Statistical analysis of high-throughput data
Integrated bioinformatic promoter- and network analysis
Systems biological simulation
Unified look-and-feel
Workflow management system
Pre-defined standard workflows
Easy integration of own tools and scripts
15. The way:
The geneXplain platform
Integrated collection of bioinformatic and systems biological
program modules („Bricks“)
Based on proven BioUML technology
Statistical analysis of high-throughput data
Integrated bioinformatic promoter- and network analysis
Systems biological simulation
Unified look-and-feel
Workflow management system
Pre-defined standard workflows
Easy integration of own tools and scripts
19. The geneXplain platform
Public Private Partnership
Clash of cultures:
Cheminformatics: commercial approaches accepted
Bioinformatics: public domain prevalent (Internet culture)
Advantages of public-domain services:
Latest state of the art
Visibility („marketing“ through publications, conference talks, etc.)
High acceptance
Disadvantages of public-domain services:
No unified look-and-feel
Low user-friendliness
Poor support
Uncertainty on side of users without expertise
Unsure long-term perspective
20. The geneXplain platform
Public Private Partnership
The disadvantages of the public domain are advantages of a
commercial offer
Optimal: combination of free and commercial tools
Business model:
Platform with integrated free and proprietary offerings
Payable access
Payable support
21. The geneXplain platform
Public Private Partnership
Advantages for the user
Standardized interface
Integrated workflows
Default parametrizations byexperts
Selection of free modules by experts in the field
Selection of proprietary, uszually low-price modules by the user
Full cost-control by the user