Eric Bonnet Computational Systems Biology of Cancer Institut Curie - INSERM U900 - Mines ParisTech
description
Transcript of Eric Bonnet Computational Systems Biology of Cancer Institut Curie - INSERM U900 - Mines ParisTech
![Page 1: Eric Bonnet Computational Systems Biology of Cancer Institut Curie - INSERM U900 - Mines ParisTech](https://reader034.fdocuments.us/reader034/viewer/2022051516/56813a4a550346895da23ec2/html5/thumbnails/1.jpg)
BiNoM 2.0, a versatile tool for accessing and analyzing pathways using standard systems biology formats
Eric BonnetComputational Systems Biology of Cancer
Institut Curie - INSERM U900 - Mines ParisTech
http://sysbio.curie.fr
Workshop NUS-IBENS 30/05/2013
![Page 2: Eric Bonnet Computational Systems Biology of Cancer Institut Curie - INSERM U900 - Mines ParisTech](https://reader034.fdocuments.us/reader034/viewer/2022051516/56813a4a550346895da23ec2/html5/thumbnails/2.jpg)
Pathway databases
![Page 3: Eric Bonnet Computational Systems Biology of Cancer Institut Curie - INSERM U900 - Mines ParisTech](https://reader034.fdocuments.us/reader034/viewer/2022051516/56813a4a550346895da23ec2/html5/thumbnails/3.jpg)
Molecular reactions maps
RB / E2F map
![Page 4: Eric Bonnet Computational Systems Biology of Cancer Institut Curie - INSERM U900 - Mines ParisTech](https://reader034.fdocuments.us/reader034/viewer/2022051516/56813a4a550346895da23ec2/html5/thumbnails/4.jpg)
Standard formats
![Page 5: Eric Bonnet Computational Systems Biology of Cancer Institut Curie - INSERM U900 - Mines ParisTech](https://reader034.fdocuments.us/reader034/viewer/2022051516/56813a4a550346895da23ec2/html5/thumbnails/5.jpg)
BiNoM, a Biological Network Manager
• Supports standard systems biology formats (BioPAX, CellDesigner, etc.).
• Facilitates the visualization and manipulation of biological networks.
• Help the user to analyze, extract and condense network information.
BiNoM Utilities
BiNoM Structure analysis
BiNoM BioPAX Query
BiNoM I/O
BiNoM BioPAXUtilities
BiNoM Modules
![Page 6: Eric Bonnet Computational Systems Biology of Cancer Institut Curie - INSERM U900 - Mines ParisTech](https://reader034.fdocuments.us/reader034/viewer/2022051516/56813a4a550346895da23ec2/html5/thumbnails/6.jpg)
Use of data from public pathway databases for modelling purposes (from Bauer-Mehren et al., Pathway databases and tools for their exploitatation: benefits, current limitations and challenges. 2009 Molecular Systems Biology 5:290).
BiNoM
![Page 7: Eric Bonnet Computational Systems Biology of Cancer Institut Curie - INSERM U900 - Mines ParisTech](https://reader034.fdocuments.us/reader034/viewer/2022051516/56813a4a550346895da23ec2/html5/thumbnails/7.jpg)
![Page 8: Eric Bonnet Computational Systems Biology of Cancer Institut Curie - INSERM U900 - Mines ParisTech](https://reader034.fdocuments.us/reader034/viewer/2022051516/56813a4a550346895da23ec2/html5/thumbnails/8.jpg)
Modular representation
RB / E2F network, 70+ proteins, 160+ reactions, 350 publications
Modular representation
![Page 9: Eric Bonnet Computational Systems Biology of Cancer Institut Curie - INSERM U900 - Mines ParisTech](https://reader034.fdocuments.us/reader034/viewer/2022051516/56813a4a550346895da23ec2/html5/thumbnails/9.jpg)
Invasive cancersNon-invasive cancers
![Page 10: Eric Bonnet Computational Systems Biology of Cancer Institut Curie - INSERM U900 - Mines ParisTech](https://reader034.fdocuments.us/reader034/viewer/2022051516/56813a4a550346895da23ec2/html5/thumbnails/10.jpg)
• Influence graph G.• Input nodes I1, I2.• Output (target) node O1.
I1 -> B -> C -> O1I1 -> E -> C -> O1I2 -> E -> C -> O1
• Combinations of Interventions:
{C}, {E, B}, {I1, I2}
• Application of OCSANA: candidate drug targets discovery.
OCSANA: Optimal Combinations of Interventions for Network Analysis
![Page 11: Eric Bonnet Computational Systems Biology of Cancer Institut Curie - INSERM U900 - Mines ParisTech](https://reader034.fdocuments.us/reader034/viewer/2022051516/56813a4a550346895da23ec2/html5/thumbnails/11.jpg)
OCSANA CI search algorithms
• Finding CIs is a combinatorial problem.
• Berge’s algorithm (1989)
• Recursive calculation of transervals on a hypergraph.
• Exact and complete, but do not scale well for networks 50+ nodes.
• Approximation solution.
• Use a score to reduce the search space.
• Score is based on the network structure.
![Page 12: Eric Bonnet Computational Systems Biology of Cancer Institut Curie - INSERM U900 - Mines ParisTech](https://reader034.fdocuments.us/reader034/viewer/2022051516/56813a4a550346895da23ec2/html5/thumbnails/12.jpg)
![Page 13: Eric Bonnet Computational Systems Biology of Cancer Institut Curie - INSERM U900 - Mines ParisTech](https://reader034.fdocuments.us/reader034/viewer/2022051516/56813a4a550346895da23ec2/html5/thumbnails/13.jpg)
BiNoM Team
Laurence Calzone
Daniel Rovera
Gautier Stoll
Paola Vera-Licona
Emmanuel Barillot
Andrei Zinovyev
http://binom.curie.fr
http://apps.cytoscape.org/apps/binom