Genostar Bioinformatics Solutions Connecting, completing and exploring biochemicaland genomic data with Metabolic Pathway Builder

ChemAxon's User Group Meeting, June 3-4th

Genostar designs and develops software and databases for analysis and exploration of genomic, proteic and metabolic data. Today were going to tell you a little bit about Genostar, and then focus on how were using the JChem 5 base in our PathwayExplorer module to identify (and predict??) links between chemical, metabolic and genomic data.

We very recently integrated JChem5 into PathwayExplorer so we are interested in your feedback.

Genostar: about usLocated in the heart of the French Alps, near Grenoble

Grenoble areaTop center for research in France, outside Paris

21,000 researchers200+ laboratories

Strong life sciences researchFrench National Institute for Research in Computer Science and Control (INRIA)Atomic Energy Research Center (CEA)Institute for Structural BiologyEuropean Molecular Biology Laboratory (EMBL)

->Genostars R&D is located near Grenoble in the French Alps. As you can see, our labs are in a beautiful area, but its not just a great area for skiing and hiking. The Grenoble area is also the largest research center in France outside of Paris with 21000 researchers and over 200 labs. In terms of life sciences research, there are biotech and medtech companies, major companies such as Becton Dickenson and BioMerieux, and large research centers. The French National Insititute for Research in Computer Science and Control (the INRIA) has 26 teams there with about 500 scientists. There is also the CEA, the Institute for Structural Biology ad the European Molecular Biology Laboratory.

We work closely with the INRIA.

Genostar: about usGenostar provides bioinformatics software, databases and analysis services for microbial research

ApplicationsVaccine discovery and developmentDrug discoveryDiagnosticsAgro-foodsEnvironment

Genostar provides bioinformatics software, databases and analysis services for microbial research: for comparative genomics, differential metabolic analyses and modeling and simulation of cellular processes.For example, from the output of next gen sequencers or the results of gene expression experiments you can map and assemble contigs, annotate or reannotate sequences and conduct differential metabolic analysis, comparing multiple organisms. You can also start with a chemical structure, identify which reactions this compound is involved in, which pathways involve those reactions and, if the pathways are complete, identify which coding regions on the genome are affected (add any other info here in terms of final results of what youre going to show later it wont hurt the audience to hear it twice).

Our software is currently used in vaccine discovery, drug discovery, diagnostics and agro-foods, as well as in academic labs and research centers around the world.

Our offer: software, data and services

ProductsMetabolic Pathway Builder suite

Perform genomic, proteic, and metabolic research with a comprehensive software suite GenoAnnot / ProteoAnnot

Perform comparative genomic and proteic sequence annotation and reannotation PathwayExplorer

Perform comparative genomic and differential metabolic analyses MicroB Database

Integrate, rigorously cross-checked genomic, proteic, biochemical and metabolic data on about 800 organisms KDB Explorer

Explore, visualize and highlight the metabolic and non-metabolic pathways specific to your organism PathwayExplorer GenoMirror

Local mirror to interactively explore KEGG data while maintaining research confidentialityServices We provide a full range of bioinformatics analysis services

Were going to be discussing JChem in the PathwayExplorer module, so this slide is just to give a quick overview PathwayExplorer is a module in the Metabolic Pathway Builder suite. We integrated Jchem 5 into PE and we are going to talk about how we are using it.

MicroB is our reference database and is updated regulalry. All the software and data are fully integrated, so that heterogeneous genomic, proteic, biochemical and metabolic data from different databanks is linked, collected and can be explored with the software.

In the same way, KDB Explorer suite allows the interactive exploration of the metabolic and non-metabolic pathways

PathwayExplorer moduleDraws on heterogeneous data into a powerful entity-relationship model

genomic (GenomeReviews, EMBL, Genbank),proteic (Swiss-Prot), classification (Enzyme, GO, NCBI taxonomy)biochemical (KEGG ligand), metabolic (KEGG pathways),expression dataComparative genomics and metabolomicsIntegrates proprietary and public methods: EC prediction, pattern inference, homologies and syntons computationsInteractive and specialized viewers

Marvin, Jchem BaseInteractively explore and visualize metabolic pathwaysCompare your own data with our reference database

Zoom in PathwayExplorerPE is dedicated to comparative genomics and metabolomics

Thanks to powerful queries and specialized viewers, biologist users can manipulate and easily explore heterogeneous data that are usually disconnected Some of specialized viewers allows the manipulation and exploration of chemical compounds to metabolism - this viewers relies on Marvin and Jchem Base.

PathwayExplorer and ChemAxon (1/4)

Run Chemaxon structural searche.g: search compounds that contain benzoate substructureManage and display chemical compoundswith MarvinExplore compoundsextracted from KEGG ligand database

There is how the PathwayExplorer interface looks like.A biologist can easily explore and visualize links between genomic, biochemical and metabolic data and organize its dataset.-> You can see there a set of compounds that come from the KEGG ligand database.

The user draw a chemical structure into the MarvinSketch editor, for instance a benzoate compound. Then the 2D structural search is run against the available chemical compounds. Once the specific set of compounds that contain the Benzoate substructure has been retrieved, the user can display it into a 2D structure panel viewer, and manipulate each compound using Marvin facilities.

PathwayExplorer and ChemAxon (2/4)

Find and display biochemical reactions that involve a benzoate derived compound

From the set of compounds that share a benzoate substructure, the user retrieves all reactions where these compounds are implied. Thanks to a powerful query builder tool, he can, for example, specify whether the compounds are substrates and/or products of these reactions.These reactions are displayed in a specific viewer that integrates Marvin facilities.

Since we use the KEGG data source that links compounds to biochemical reactions, and the PathwayExplorer module keep these links after the KEGG data has been loaded it is possible to explore biochemical from a powerful PE query builder tool.

PathwayExplorer and ChemAxon (3/4)

PathwayExplorer allow to manipulate KEGG maps which are made up of pathways over well known metabolism processes.

Boxes show reactions that are possibly catalized by an enzyme.Circles show compounds.Arrows show the direction of the reaction. We develop tools to make KEGG maps interactive for the userHere you can see the KEGG map of the Phenylalanin, Tyrosine and Tryptophan biosynthesis where reactions that implied compounds with a benzoate substructure are highlighted in blue.

Furthermore, reactions can be colorized according to the organism they belong to:

Green reactions belongs to the Bacillus subtilisRed one belongs to the Listeria innocua

Indeed, you can load and connect biological data of any microbial organism from our reference database, MicroB.These organisms are more or less similar according to the taxonomic classification.

Then the user can select an interesting metabolic pathway into the KEGG mapThanks to a tool available in the KEGG map toolbar, he retrieves the genes that code these enzymes.

PathwayExplorer and ChemAxon (4/4)

Compare syntenic regions1 operon in Bacillus2 operons in Listeria

The collected genes coming from the previous pathway selectionare displayed in genomic maps of both organism.

You can see the Bacillus subtilis chromosome where the selected genes are highlighted in greenYou can see the Listeria innocua chromosome where the selected genes are highlighted in red

This comparative analysis identified a chromosical reorganization between the 2 chromosomes.

PerspectivesExtend Metabolic Pathway Builder capacities further in the direction of cheminformatics

Increase connections to external biochemical and chemical databases (ChEBI and UniPathway, PubChem)Integrate 3D facilities (PDB, PubChem, MarvinSpace)Implement structural analysis, predict molecular properties(Calculator Plugins - Chemical Terms)Extend partnerships to increase our capacity in drug discovery and molecular design

We would like

Thank you

Partners

Contact

Pierre-Emmanuel Cironciron@genostar.com+33 476 97 10 74

Sophie Huet sophie.huet@genostar.com+33 476 97 10 78

Adrienne Kennardadrienne.kennard@genostar.cominfo@genostar.comwww.genostar.com

Thank you for your attentionAnd feel free to ask any question

Genostar designs and develops software and databases for analysis and exploration of genomic, proteic and metabolic data. Today were going to tell you a little bit about Genostar, and then focus on how were using the JChem 5 base in our PathwayExplorer module to identify (and predict??) links between chemical, metabolic and genomic data.

We very recently integrated JChem5 into PathwayExplorer so we are interested in your feedback.

->Genostars R&D is located near Grenoble in the French Alps. As you can see, our labs are in a beautiful area, but its not just a great area for skiing and hiking. The Grenoble area is also the largest research center in France outside of Paris with 21000 researchers and over 200 labs. In terms of life sciences research, there are biotech and medtech companies, major companies such as Becton Dickenson and BioMerieux, and large research centers. The French National Insititute for Research in Computer Science and Control (the INRIA) has 26 teams there with about 500 scientists. There is also the CEA, the Institute for Structural Biology ad the European Molecular Biology Laboratory.

We work closely with the INRIA.Genostar provides bioinformatics software, databases and analysis services for microbial research: for comparative genomics, differential metabolic analyses and modeling and simulation of cellular processes.For example, from the output of next gen sequencers or the results of gene expression experiments you can map and assemble contigs, annotate or reannotate sequences and conduct differential metabolic analysis, comparing multiple organisms. You can also start with a chemical structure, identify which reactions this compound is involved in, which pathways involve those reactions and, if the pathways are complete, identify which coding regions on the genome are affected (add any other info here in terms of final results of what youre going to show later it wont hurt the audience to hear it twice).

Our software is currently used in vaccine discovery, drug discovery, diagnostics and agro-foods, as well as in academic labs and research centers around the world.Were going to be discussing JChem in the PathwayExplorer module, so this slide is just to give a quick overview PathwayExplorer is a module in the Metabolic Pathway Builder suite. We integrated Jchem 5 into PE and we are going to talk about how we are using it.

MicroB is our reference database and is updated regulalry. All the software and data are fully integrated, so that heterogeneous genomic, proteic, biochemical and metabolic data from different databanks is linked, collected and can be explored with the software.

In the same way, KDB Explorer suite allows the interactive exploration of the metabolic and non-metabolic pathwaysZoom in PathwayExplorerPE is dedicated to comparative genomics and metabolomics

Thanks to powerful queries and specialized viewers, biologist users can manipulate and easily explore heterogeneous data that are usually disconnected Some of specialized viewers allows the manipulation and exploration of chemical compounds to metabolism - this viewers relies on Marvin and Jchem Base.There is how the PathwayExplorer interface looks like.A biologist can easily explore and visualize links between genomic, biochemical and metabolic data and organize its dataset.-> You can see there a set of compounds that come from the KEGG ligand database.

The user draw a chemical structure into the MarvinSketch editor, for instance a benzoate compound. Then the 2D structural search is run against the available chemical compounds. Once the specific set of compounds that contain the Benzoate substructure has been retrieved, the user can display it into a 2D structure panel viewer, and manipulate each compound using Marvin facilities.

From the set of compounds that share a benzoate substructure, the user retrieves all reactions where these compounds are implied. Thanks to a powerful query builder tool, he can, for example, specify whether the compounds are substrates and/or products of these reactions.These reactions are displayed in a specific viewer that integrates Marvin facilities.

Since we use the KEGG data source that links compounds to biochemical reactions, and the PathwayExplorer module keep these links after the KEGG data has been loaded it is possible to explore biochemical from a powerful PE query builder tool. PathwayExplorer allow to manipulate KEGG maps which are made up of pathways over well known metabolism processes.

Boxes show reactions that are possibly catalized by an enzyme.Circles show compounds.Arrows show the direction of the reaction. We develop tools to make KEGG maps interactive for the userHere you can see the KEGG map of the Phenylalanin, Tyrosine and Tryptophan biosynthesis where reactions that implied compounds with a benzoate substructure are highlighted in blue.

Furthermore, reactions can be colorized according to the organism they belong to:

Green reactions belongs to the Bacillus subtilisRed one belongs to the Listeria innocua

Indeed, you can load and connect biological data of any microbial organism from our reference database, MicroB.These organisms are more or less similar according to the taxonomic classification.

Then the user can select an interesting metabolic pathway into the KEGG mapThanks to a tool available in the KEGG map toolbar, he retrieves the genes that code these enzymes.The collected genes coming from the previous pathway selectionare displayed in genomic maps of both organism.

You can see the Bacillus subtilis chromosome where the selected genes are highlighted in greenYou can see the Listeria innocua chromosome where the selected genes are highlighted in red

This comparative analysis identified a chromosical reorganization between the 2 chromosomes.We would likeThank you for your attentionAnd feel free to ask any question