SlideShare uma empresa Scribd logo
1 de 29
Baixar para ler offline
Network Visualization and Analysis
in the cBio Cancer Genomics Portal
     U. Dogrusoz, S.O. Sumer, S. Sonlu, J. Gao, B.A. Aksoy,
          B.E. Gross, N. Schultz, E. Cerami, C. Sander
cBio Cancer Genomics Portal



Goal:
Make complex genomic data available through an intuitive interface
Allow explorative data analysis / hypothesis testing / visualization




                                         Cerami et al. 2012, Cancer Discovery
NetBioSIG2012 ugurdogrusoz-cbio
cBio Cancer Genomics Portal




                 Cerami et al. 2012, Cancer Discovery
Workflow of network analysis
Pathway Commons




           Cerami et al 2010, Nucl Acids Res
Workflow of network analysis
Hairball Problem




            Complete network for TP53, MDM2, MDM4
            & CDKN2A (463 interacting neighbors)
This complete network can be downloaded in SIF or GraphML in cBio Portal.
Pre-filtered network based on alteration frequencies



      The network below contains 54 nodes, including
      your 4 query genes and the 50 most frequently
                       genes out 463
      altered neighbor genes(out of 463).




   Query genes: CDKN2A MDM2 MDM4 TP53
Workflow of network analysis
Genomic data overlaid on interaction network
Genomic data overlaid on interaction network




Alteration frequency: the % of samples that were altered on the gene
Genomic data overlaid on interaction network

                            Color gradient
                            •white to red
                            •based on alteration
                            frequency



Genomic data
•mutation
•copy number
•mRNA expression
Further filtering by genomic alterations
                 Filter genes by alteration frequency




                              Slide to
                              threshold          Or type
                              value              threshold
                                                 value
Further filtering by genomic alterations
                 Gene with total alteration frequency
                 12% or less filtered out
Filtering by genes of interest
                   Hide selected genes
                   from the network



                                            Search genes
                                            by name




                      Select genes from
                      canvas or gene list
                      under Genes tab
Filtering by interaction type & source

                  Interactions       Interactions
                  merged by
                  default



                                    Type (color-coded)
                                    & source shown in
                                    interaction details
   Shown
   individually
Filtering by interaction type & source
Filtering by interaction type & source
Automatic network layout

                            Change layout
Recalculate                 options
layout

Recalculate
layout after
filtering
Iterative network analysis




                             Re-submit
                             selected genes
                             to the portal
Drugs of     New cBioPortal features
specified genes
              Drug – gene targeting
   • Data source is DrugBank database of detail:
                                   Level
     (http://www.drugbank.ca) -None
Inspect details targeting specified-FDA approved only
   • Only drugs                     genes shown
including:                         -All
-Targeted genes
-Corresponding
DrugBank page
Other new cBioPortal features
 Network visualization service for IGV
• Glioblastoma, RB pathway
Other new cBioPortal features
     Cross-cancer query
Other new cBioPortal features
       Oncoprint improvements
Protein/phosphoprotein    Mutation details
       event call
Other new cBioPortal features
     Mutation diagram
Other new cBioPortal features
       Many new cancer studies
• 21 (5 of them published, rest provisional)
  cancer studies
Work in progress and future plans
• SBGN-compliant viewer (GSoC)
   – Networks presented in SBGN Process Description
     language
• Construct Network-of-Interest from Genes-of-
  Interest using linker paths (Dogrusoz et al, 2009, BMC Bioinf)
• Roundtrip analysis (query, modify, re-query, …)
• Better/incremental layout
• Use Cytoscape Web 2 (html5 version)
Acknowledgements
• Bilkent University    • MSKCC
  – S. Onur Sumer         – S. Onur Sumer
  – Sinan Sonlu           – Jianjiong Gao
  – Naim Kucukdemirci     – B. Arman Aksoy
  – Istemi Bahceci        – Benjamin E. Gross
                          – Nikolaus Schultz
                          – Ethan Cerami
                          – Chris Sander

Mais conteúdo relacionado

Mais procurados

NetBioSIG2014-Talk by Hyunghoon Cho
NetBioSIG2014-Talk by Hyunghoon ChoNetBioSIG2014-Talk by Hyunghoon Cho
NetBioSIG2014-Talk by Hyunghoon ChoAlexander Pico
 
AI in Bioinformatics
AI in BioinformaticsAI in Bioinformatics
AI in BioinformaticsAli Kishk
 
Project report-on-bio-informatics
Project report-on-bio-informaticsProject report-on-bio-informatics
Project report-on-bio-informaticsDaniela Rotariu
 
EnrichNet: Graph-based statistic and web-application for gene/protein set enr...
EnrichNet: Graph-based statistic and web-application for gene/protein set enr...EnrichNet: Graph-based statistic and web-application for gene/protein set enr...
EnrichNet: Graph-based statistic and web-application for gene/protein set enr...Enrico Glaab
 
Metabolic Network Analysis
Metabolic Network AnalysisMetabolic Network Analysis
Metabolic Network AnalysisMas Kot
 
NetBioSIG2013-Talk Tijana Milenkovic
NetBioSIG2013-Talk Tijana MilenkovicNetBioSIG2013-Talk Tijana Milenkovic
NetBioSIG2013-Talk Tijana MilenkovicAlexander Pico
 
NetBioSIG2013-Talk Vuk Janjic
NetBioSIG2013-Talk Vuk JanjicNetBioSIG2013-Talk Vuk Janjic
NetBioSIG2013-Talk Vuk JanjicAlexander Pico
 
NetBioSIG2014-Talk by Tijana Milenkovic
NetBioSIG2014-Talk by Tijana MilenkovicNetBioSIG2014-Talk by Tijana Milenkovic
NetBioSIG2014-Talk by Tijana MilenkovicAlexander Pico
 
NetBioSIG2013-Talk Gang Su
NetBioSIG2013-Talk Gang SuNetBioSIG2013-Talk Gang Su
NetBioSIG2013-Talk Gang SuAlexander Pico
 
Novel network pharmacology methods for drug mechanism of action identificatio...
Novel network pharmacology methods for drug mechanism of action identificatio...Novel network pharmacology methods for drug mechanism of action identificatio...
Novel network pharmacology methods for drug mechanism of action identificatio...laserxiong
 
Martin Ringwald, Mouse Gene Expression DB, fged_seattle_2013
Martin Ringwald, Mouse Gene Expression DB, fged_seattle_2013Martin Ringwald, Mouse Gene Expression DB, fged_seattle_2013
Martin Ringwald, Mouse Gene Expression DB, fged_seattle_2013Functional Genomics Data Society
 
System biology and its tools
System biology and its toolsSystem biology and its tools
System biology and its toolsGaurav Diwakar
 
Bioinformatic, and tools by kk sahu
Bioinformatic, and tools by kk sahuBioinformatic, and tools by kk sahu
Bioinformatic, and tools by kk sahuKAUSHAL SAHU
 
Basics of Data Analysis in Bioinformatics
Basics of Data Analysis in BioinformaticsBasics of Data Analysis in Bioinformatics
Basics of Data Analysis in BioinformaticsElena Sügis
 

Mais procurados (20)

NetBioSIG2014-Talk by Hyunghoon Cho
NetBioSIG2014-Talk by Hyunghoon ChoNetBioSIG2014-Talk by Hyunghoon Cho
NetBioSIG2014-Talk by Hyunghoon Cho
 
AI in Bioinformatics
AI in BioinformaticsAI in Bioinformatics
AI in Bioinformatics
 
Project report-on-bio-informatics
Project report-on-bio-informaticsProject report-on-bio-informatics
Project report-on-bio-informatics
 
EnrichNet: Graph-based statistic and web-application for gene/protein set enr...
EnrichNet: Graph-based statistic and web-application for gene/protein set enr...EnrichNet: Graph-based statistic and web-application for gene/protein set enr...
EnrichNet: Graph-based statistic and web-application for gene/protein set enr...
 
Metabolic Network Analysis
Metabolic Network AnalysisMetabolic Network Analysis
Metabolic Network Analysis
 
Michael Reich, GenomeSpace Workshop, fged_seattle_2013
Michael Reich, GenomeSpace Workshop, fged_seattle_2013Michael Reich, GenomeSpace Workshop, fged_seattle_2013
Michael Reich, GenomeSpace Workshop, fged_seattle_2013
 
NetBioSIG2013-Talk Tijana Milenkovic
NetBioSIG2013-Talk Tijana MilenkovicNetBioSIG2013-Talk Tijana Milenkovic
NetBioSIG2013-Talk Tijana Milenkovic
 
presentation
presentationpresentation
presentation
 
Bioinformatics
BioinformaticsBioinformatics
Bioinformatics
 
Bioinformatics
BioinformaticsBioinformatics
Bioinformatics
 
NetBioSIG2013-Talk Vuk Janjic
NetBioSIG2013-Talk Vuk JanjicNetBioSIG2013-Talk Vuk Janjic
NetBioSIG2013-Talk Vuk Janjic
 
NetBioSIG2014-Talk by Tijana Milenkovic
NetBioSIG2014-Talk by Tijana MilenkovicNetBioSIG2014-Talk by Tijana Milenkovic
NetBioSIG2014-Talk by Tijana Milenkovic
 
NetBioSIG2013-Talk Gang Su
NetBioSIG2013-Talk Gang SuNetBioSIG2013-Talk Gang Su
NetBioSIG2013-Talk Gang Su
 
Novel network pharmacology methods for drug mechanism of action identificatio...
Novel network pharmacology methods for drug mechanism of action identificatio...Novel network pharmacology methods for drug mechanism of action identificatio...
Novel network pharmacology methods for drug mechanism of action identificatio...
 
Martin Ringwald, Mouse Gene Expression DB, fged_seattle_2013
Martin Ringwald, Mouse Gene Expression DB, fged_seattle_2013Martin Ringwald, Mouse Gene Expression DB, fged_seattle_2013
Martin Ringwald, Mouse Gene Expression DB, fged_seattle_2013
 
System biology and its tools
System biology and its toolsSystem biology and its tools
System biology and its tools
 
Cshl minseqe 2013_ouellette
Cshl minseqe 2013_ouelletteCshl minseqe 2013_ouellette
Cshl minseqe 2013_ouellette
 
Bioinformatic, and tools by kk sahu
Bioinformatic, and tools by kk sahuBioinformatic, and tools by kk sahu
Bioinformatic, and tools by kk sahu
 
Qi liu 08.08.2014
Qi liu 08.08.2014Qi liu 08.08.2014
Qi liu 08.08.2014
 
Basics of Data Analysis in Bioinformatics
Basics of Data Analysis in BioinformaticsBasics of Data Analysis in Bioinformatics
Basics of Data Analysis in Bioinformatics
 

Semelhante a NetBioSIG2012 ugurdogrusoz-cbio

cBio Cancer Genomics Portal: Network View
cBio Cancer Genomics Portal:  Network ViewcBio Cancer Genomics Portal:  Network View
cBio Cancer Genomics Portal: Network ViewEthan Cerami
 
CRISPR Screening: the What, Why and How
CRISPR Screening: the What, Why and HowCRISPR Screening: the What, Why and How
CRISPR Screening: the What, Why and HowHorizonDiscovery
 
Mar2013 Performance Metrics Working Group
Mar2013 Performance Metrics Working GroupMar2013 Performance Metrics Working Group
Mar2013 Performance Metrics Working GroupGenomeInABottle
 
Genome Browsing, Genomic Data Mining and Genome Data Visualization with Ensem...
Genome Browsing, Genomic Data Mining and Genome Data Visualization with Ensem...Genome Browsing, Genomic Data Mining and Genome Data Visualization with Ensem...
Genome Browsing, Genomic Data Mining and Genome Data Visualization with Ensem...VHIR Vall d’Hebron Institut de Recerca
 
Informal presentation on bioinformatics
Informal presentation on bioinformaticsInformal presentation on bioinformatics
Informal presentation on bioinformaticsAtai Rabby
 
Rewriting the Genome Using CRISPR and Synthetic Biology
Rewriting the Genome Using CRISPR and Synthetic Biology Rewriting the Genome Using CRISPR and Synthetic Biology
Rewriting the Genome Using CRISPR and Synthetic Biology Integrated DNA Technologies
 
Visual Exploration of Clinical and Genomic Data for Patient Stratification
Visual Exploration of Clinical and Genomic Data for Patient StratificationVisual Exploration of Clinical and Genomic Data for Patient Stratification
Visual Exploration of Clinical and Genomic Data for Patient StratificationNils Gehlenborg
 
Kim Pruitt trainingbiocuration2015
Kim Pruitt trainingbiocuration2015Kim Pruitt trainingbiocuration2015
Kim Pruitt trainingbiocuration2015Kim D. Pruitt
 
Genome in a Bottle - Towards new benchmarks for the “dark matter” of the huma...
Genome in a Bottle - Towards new benchmarks for the “dark matter” of the huma...Genome in a Bottle - Towards new benchmarks for the “dark matter” of the huma...
Genome in a Bottle - Towards new benchmarks for the “dark matter” of the huma...GenomeInABottle
 
GIAB update for GRC GIAB workshop 191015
GIAB update for GRC GIAB workshop 191015GIAB update for GRC GIAB workshop 191015
GIAB update for GRC GIAB workshop 191015GenomeInABottle
 
Multi-scale network biology model & the model library
Multi-scale network biology model & the model libraryMulti-scale network biology model & the model library
Multi-scale network biology model & the model librarylaserxiong
 
Giab for jax long read 190917
Giab for jax long read 190917Giab for jax long read 190917
Giab for jax long read 190917GenomeInABottle
 
20100509 bioinformatics kapushesky_lecture03-04_0
20100509 bioinformatics kapushesky_lecture03-04_020100509 bioinformatics kapushesky_lecture03-04_0
20100509 bioinformatics kapushesky_lecture03-04_0Computer Science Club
 
GIAB Integrating multiple technologies to form benchmark SVs 180517
GIAB Integrating multiple technologies to form benchmark SVs 180517GIAB Integrating multiple technologies to form benchmark SVs 180517
GIAB Integrating multiple technologies to form benchmark SVs 180517GenomeInABottle
 

Semelhante a NetBioSIG2012 ugurdogrusoz-cbio (20)

cBio Cancer Genomics Portal: Network View
cBio Cancer Genomics Portal:  Network ViewcBio Cancer Genomics Portal:  Network View
cBio Cancer Genomics Portal: Network View
 
CRISPR Screening: the What, Why and How
CRISPR Screening: the What, Why and HowCRISPR Screening: the What, Why and How
CRISPR Screening: the What, Why and How
 
PhD midterm report
PhD midterm reportPhD midterm report
PhD midterm report
 
Mar2013 Performance Metrics Working Group
Mar2013 Performance Metrics Working GroupMar2013 Performance Metrics Working Group
Mar2013 Performance Metrics Working Group
 
Gnc march 2012
Gnc march 2012Gnc march 2012
Gnc march 2012
 
Slas2012 Whoeck
Slas2012 WhoeckSlas2012 Whoeck
Slas2012 Whoeck
 
Genome Browsing, Genomic Data Mining and Genome Data Visualization with Ensem...
Genome Browsing, Genomic Data Mining and Genome Data Visualization with Ensem...Genome Browsing, Genomic Data Mining and Genome Data Visualization with Ensem...
Genome Browsing, Genomic Data Mining and Genome Data Visualization with Ensem...
 
Variant analysis and whole exome sequencing
Variant analysis and whole exome sequencingVariant analysis and whole exome sequencing
Variant analysis and whole exome sequencing
 
Informal presentation on bioinformatics
Informal presentation on bioinformaticsInformal presentation on bioinformatics
Informal presentation on bioinformatics
 
Rewriting the Genome Using CRISPR and Synthetic Biology
Rewriting the Genome Using CRISPR and Synthetic Biology Rewriting the Genome Using CRISPR and Synthetic Biology
Rewriting the Genome Using CRISPR and Synthetic Biology
 
Visual Exploration of Clinical and Genomic Data for Patient Stratification
Visual Exploration of Clinical and Genomic Data for Patient StratificationVisual Exploration of Clinical and Genomic Data for Patient Stratification
Visual Exploration of Clinical and Genomic Data for Patient Stratification
 
Kim Pruitt trainingbiocuration2015
Kim Pruitt trainingbiocuration2015Kim Pruitt trainingbiocuration2015
Kim Pruitt trainingbiocuration2015
 
Genome in a Bottle - Towards new benchmarks for the “dark matter” of the huma...
Genome in a Bottle - Towards new benchmarks for the “dark matter” of the huma...Genome in a Bottle - Towards new benchmarks for the “dark matter” of the huma...
Genome in a Bottle - Towards new benchmarks for the “dark matter” of the huma...
 
Genomic Databases-.pptx
Genomic Databases-.pptxGenomic Databases-.pptx
Genomic Databases-.pptx
 
GIAB update for GRC GIAB workshop 191015
GIAB update for GRC GIAB workshop 191015GIAB update for GRC GIAB workshop 191015
GIAB update for GRC GIAB workshop 191015
 
Multi-scale network biology model & the model library
Multi-scale network biology model & the model libraryMulti-scale network biology model & the model library
Multi-scale network biology model & the model library
 
Cytoscape Talk 2010
Cytoscape Talk 2010Cytoscape Talk 2010
Cytoscape Talk 2010
 
Giab for jax long read 190917
Giab for jax long read 190917Giab for jax long read 190917
Giab for jax long read 190917
 
20100509 bioinformatics kapushesky_lecture03-04_0
20100509 bioinformatics kapushesky_lecture03-04_020100509 bioinformatics kapushesky_lecture03-04_0
20100509 bioinformatics kapushesky_lecture03-04_0
 
GIAB Integrating multiple technologies to form benchmark SVs 180517
GIAB Integrating multiple technologies to form benchmark SVs 180517GIAB Integrating multiple technologies to form benchmark SVs 180517
GIAB Integrating multiple technologies to form benchmark SVs 180517
 

Mais de Alexander Pico

NRNB Annual Report 2018
NRNB Annual Report 2018NRNB Annual Report 2018
NRNB Annual Report 2018Alexander Pico
 
NRNB Annual Report 2017
NRNB Annual Report 2017NRNB Annual Report 2017
NRNB Annual Report 2017Alexander Pico
 
2016 Cytoscape 3.3 Tutorial
2016 Cytoscape 3.3 Tutorial2016 Cytoscape 3.3 Tutorial
2016 Cytoscape 3.3 TutorialAlexander Pico
 
NRNB Annual Report 2016: Overall
NRNB Annual Report 2016: OverallNRNB Annual Report 2016: Overall
NRNB Annual Report 2016: OverallAlexander Pico
 
Technology R&D Theme 2: From Descriptive to Predictive Networks
Technology R&D Theme 2: From Descriptive to Predictive NetworksTechnology R&D Theme 2: From Descriptive to Predictive Networks
Technology R&D Theme 2: From Descriptive to Predictive NetworksAlexander Pico
 
Overall Vision for NRNB: 2015-2020
Overall Vision for NRNB: 2015-2020Overall Vision for NRNB: 2015-2020
Overall Vision for NRNB: 2015-2020Alexander Pico
 
2015 Cytoscape 3.2 Tutorial
2015 Cytoscape 3.2 Tutorial2015 Cytoscape 3.2 Tutorial
2015 Cytoscape 3.2 TutorialAlexander Pico
 
NetBioSIG2014-FlashJournalClub by Frank Kramer
NetBioSIG2014-FlashJournalClub by Frank KramerNetBioSIG2014-FlashJournalClub by Frank Kramer
NetBioSIG2014-FlashJournalClub by Frank KramerAlexander Pico
 
NetBioSIG2014-Talk by Salvatore Loguercio
NetBioSIG2014-Talk by Salvatore LoguercioNetBioSIG2014-Talk by Salvatore Loguercio
NetBioSIG2014-Talk by Salvatore LoguercioAlexander Pico
 
NetBioSIG2014-Intro by Alex Pico
NetBioSIG2014-Intro by Alex PicoNetBioSIG2014-Intro by Alex Pico
NetBioSIG2014-Intro by Alex PicoAlexander Pico
 
NetBioSIG2014-Talk by Traver Hart
NetBioSIG2014-Talk by Traver HartNetBioSIG2014-Talk by Traver Hart
NetBioSIG2014-Talk by Traver HartAlexander Pico
 
NetBioSIG2014-Talk by Yu Xia
NetBioSIG2014-Talk by Yu XiaNetBioSIG2014-Talk by Yu Xia
NetBioSIG2014-Talk by Yu XiaAlexander Pico
 
NetBioSIG2014-Keynote by Marian Walhout
NetBioSIG2014-Keynote by Marian WalhoutNetBioSIG2014-Keynote by Marian Walhout
NetBioSIG2014-Keynote by Marian WalhoutAlexander Pico
 
NetBioSIG2014-Talk by Ashwini Patil
NetBioSIG2014-Talk by Ashwini PatilNetBioSIG2014-Talk by Ashwini Patil
NetBioSIG2014-Talk by Ashwini PatilAlexander Pico
 
NetBioSIG2014-Talk by Gerald Quon
NetBioSIG2014-Talk by Gerald QuonNetBioSIG2014-Talk by Gerald Quon
NetBioSIG2014-Talk by Gerald QuonAlexander Pico
 
Visualization and Analysis of Dynamic Networks
Visualization and Analysis of Dynamic Networks Visualization and Analysis of Dynamic Networks
Visualization and Analysis of Dynamic Networks Alexander Pico
 
NRNB Annual Report 2013
NRNB Annual Report 2013NRNB Annual Report 2013
NRNB Annual Report 2013Alexander Pico
 
Introduction to WikiPathways
Introduction to WikiPathwaysIntroduction to WikiPathways
Introduction to WikiPathwaysAlexander Pico
 
Network Visualization and Analysis with Cytoscape
Network Visualization and Analysis with CytoscapeNetwork Visualization and Analysis with Cytoscape
Network Visualization and Analysis with CytoscapeAlexander Pico
 
NetBioSIG2013-KEYNOTE Michael Schroeder
NetBioSIG2013-KEYNOTE Michael SchroederNetBioSIG2013-KEYNOTE Michael Schroeder
NetBioSIG2013-KEYNOTE Michael SchroederAlexander Pico
 

Mais de Alexander Pico (20)

NRNB Annual Report 2018
NRNB Annual Report 2018NRNB Annual Report 2018
NRNB Annual Report 2018
 
NRNB Annual Report 2017
NRNB Annual Report 2017NRNB Annual Report 2017
NRNB Annual Report 2017
 
2016 Cytoscape 3.3 Tutorial
2016 Cytoscape 3.3 Tutorial2016 Cytoscape 3.3 Tutorial
2016 Cytoscape 3.3 Tutorial
 
NRNB Annual Report 2016: Overall
NRNB Annual Report 2016: OverallNRNB Annual Report 2016: Overall
NRNB Annual Report 2016: Overall
 
Technology R&D Theme 2: From Descriptive to Predictive Networks
Technology R&D Theme 2: From Descriptive to Predictive NetworksTechnology R&D Theme 2: From Descriptive to Predictive Networks
Technology R&D Theme 2: From Descriptive to Predictive Networks
 
Overall Vision for NRNB: 2015-2020
Overall Vision for NRNB: 2015-2020Overall Vision for NRNB: 2015-2020
Overall Vision for NRNB: 2015-2020
 
2015 Cytoscape 3.2 Tutorial
2015 Cytoscape 3.2 Tutorial2015 Cytoscape 3.2 Tutorial
2015 Cytoscape 3.2 Tutorial
 
NetBioSIG2014-FlashJournalClub by Frank Kramer
NetBioSIG2014-FlashJournalClub by Frank KramerNetBioSIG2014-FlashJournalClub by Frank Kramer
NetBioSIG2014-FlashJournalClub by Frank Kramer
 
NetBioSIG2014-Talk by Salvatore Loguercio
NetBioSIG2014-Talk by Salvatore LoguercioNetBioSIG2014-Talk by Salvatore Loguercio
NetBioSIG2014-Talk by Salvatore Loguercio
 
NetBioSIG2014-Intro by Alex Pico
NetBioSIG2014-Intro by Alex PicoNetBioSIG2014-Intro by Alex Pico
NetBioSIG2014-Intro by Alex Pico
 
NetBioSIG2014-Talk by Traver Hart
NetBioSIG2014-Talk by Traver HartNetBioSIG2014-Talk by Traver Hart
NetBioSIG2014-Talk by Traver Hart
 
NetBioSIG2014-Talk by Yu Xia
NetBioSIG2014-Talk by Yu XiaNetBioSIG2014-Talk by Yu Xia
NetBioSIG2014-Talk by Yu Xia
 
NetBioSIG2014-Keynote by Marian Walhout
NetBioSIG2014-Keynote by Marian WalhoutNetBioSIG2014-Keynote by Marian Walhout
NetBioSIG2014-Keynote by Marian Walhout
 
NetBioSIG2014-Talk by Ashwini Patil
NetBioSIG2014-Talk by Ashwini PatilNetBioSIG2014-Talk by Ashwini Patil
NetBioSIG2014-Talk by Ashwini Patil
 
NetBioSIG2014-Talk by Gerald Quon
NetBioSIG2014-Talk by Gerald QuonNetBioSIG2014-Talk by Gerald Quon
NetBioSIG2014-Talk by Gerald Quon
 
Visualization and Analysis of Dynamic Networks
Visualization and Analysis of Dynamic Networks Visualization and Analysis of Dynamic Networks
Visualization and Analysis of Dynamic Networks
 
NRNB Annual Report 2013
NRNB Annual Report 2013NRNB Annual Report 2013
NRNB Annual Report 2013
 
Introduction to WikiPathways
Introduction to WikiPathwaysIntroduction to WikiPathways
Introduction to WikiPathways
 
Network Visualization and Analysis with Cytoscape
Network Visualization and Analysis with CytoscapeNetwork Visualization and Analysis with Cytoscape
Network Visualization and Analysis with Cytoscape
 
NetBioSIG2013-KEYNOTE Michael Schroeder
NetBioSIG2013-KEYNOTE Michael SchroederNetBioSIG2013-KEYNOTE Michael Schroeder
NetBioSIG2013-KEYNOTE Michael Schroeder
 

Último

P4C x ELT = P4ELT: Its Theoretical Background (Kanazawa, 2024 March).pdf
P4C x ELT = P4ELT: Its Theoretical Background (Kanazawa, 2024 March).pdfP4C x ELT = P4ELT: Its Theoretical Background (Kanazawa, 2024 March).pdf
P4C x ELT = P4ELT: Its Theoretical Background (Kanazawa, 2024 March).pdfYu Kanazawa / Osaka University
 
How to Manage Cross-Selling in Odoo 17 Sales
How to Manage Cross-Selling in Odoo 17 SalesHow to Manage Cross-Selling in Odoo 17 Sales
How to Manage Cross-Selling in Odoo 17 SalesCeline George
 
10 Topics For MBA Project Report [HR].pdf
10 Topics For MBA Project Report [HR].pdf10 Topics For MBA Project Report [HR].pdf
10 Topics For MBA Project Report [HR].pdfJayanti Pande
 
ARTICULAR DISC OF TEMPOROMANDIBULAR JOINT
ARTICULAR DISC OF TEMPOROMANDIBULAR JOINTARTICULAR DISC OF TEMPOROMANDIBULAR JOINT
ARTICULAR DISC OF TEMPOROMANDIBULAR JOINTDR. SNEHA NAIR
 
Clinical Pharmacy Introduction to Clinical Pharmacy, Concept of clinical pptx
Clinical Pharmacy  Introduction to Clinical Pharmacy, Concept of clinical pptxClinical Pharmacy  Introduction to Clinical Pharmacy, Concept of clinical pptx
Clinical Pharmacy Introduction to Clinical Pharmacy, Concept of clinical pptxraviapr7
 
Prescribed medication order and communication skills.pptx
Prescribed medication order and communication skills.pptxPrescribed medication order and communication skills.pptx
Prescribed medication order and communication skills.pptxraviapr7
 
How to Show Error_Warning Messages in Odoo 17
How to Show Error_Warning Messages in Odoo 17How to Show Error_Warning Messages in Odoo 17
How to Show Error_Warning Messages in Odoo 17Celine George
 
How to Send Emails From Odoo 17 Using Code
How to Send Emails From Odoo 17 Using CodeHow to Send Emails From Odoo 17 Using Code
How to Send Emails From Odoo 17 Using CodeCeline George
 
Ultra structure and life cycle of Plasmodium.pptx
Ultra structure and life cycle of Plasmodium.pptxUltra structure and life cycle of Plasmodium.pptx
Ultra structure and life cycle of Plasmodium.pptxDr. Asif Anas
 
AUDIENCE THEORY -- FANDOM -- JENKINS.pptx
AUDIENCE THEORY -- FANDOM -- JENKINS.pptxAUDIENCE THEORY -- FANDOM -- JENKINS.pptx
AUDIENCE THEORY -- FANDOM -- JENKINS.pptxiammrhaywood
 
How to Add Existing Field in One2Many Tree View in Odoo 17
How to Add Existing Field in One2Many Tree View in Odoo 17How to Add Existing Field in One2Many Tree View in Odoo 17
How to Add Existing Field in One2Many Tree View in Odoo 17Celine George
 
How to Make a Field read-only in Odoo 17
How to Make a Field read-only in Odoo 17How to Make a Field read-only in Odoo 17
How to Make a Field read-only in Odoo 17Celine George
 
The Stolen Bacillus by Herbert George Wells
The Stolen Bacillus by Herbert George WellsThe Stolen Bacillus by Herbert George Wells
The Stolen Bacillus by Herbert George WellsEugene Lysak
 
Easter in the USA presentation by Chloe.
Easter in the USA presentation by Chloe.Easter in the USA presentation by Chloe.
Easter in the USA presentation by Chloe.EnglishCEIPdeSigeiro
 
KARNAADA.pptx made by - saransh dwivedi ( SD ) - SHALAKYA TANTRA - ENT - 4...
KARNAADA.pptx  made by -  saransh dwivedi ( SD ) -  SHALAKYA TANTRA - ENT - 4...KARNAADA.pptx  made by -  saransh dwivedi ( SD ) -  SHALAKYA TANTRA - ENT - 4...
KARNAADA.pptx made by - saransh dwivedi ( SD ) - SHALAKYA TANTRA - ENT - 4...M56BOOKSTORE PRODUCT/SERVICE
 
3.26.24 Race, the Draft, and the Vietnam War.pptx
3.26.24 Race, the Draft, and the Vietnam War.pptx3.26.24 Race, the Draft, and the Vietnam War.pptx
3.26.24 Race, the Draft, and the Vietnam War.pptxmary850239
 
Drug Information Services- DIC and Sources.
Drug Information Services- DIC and Sources.Drug Information Services- DIC and Sources.
Drug Information Services- DIC and Sources.raviapr7
 
CHUYÊN ĐỀ DẠY THÊM TIẾNG ANH LỚP 11 - GLOBAL SUCCESS - NĂM HỌC 2023-2024 - HK...
CHUYÊN ĐỀ DẠY THÊM TIẾNG ANH LỚP 11 - GLOBAL SUCCESS - NĂM HỌC 2023-2024 - HK...CHUYÊN ĐỀ DẠY THÊM TIẾNG ANH LỚP 11 - GLOBAL SUCCESS - NĂM HỌC 2023-2024 - HK...
CHUYÊN ĐỀ DẠY THÊM TIẾNG ANH LỚP 11 - GLOBAL SUCCESS - NĂM HỌC 2023-2024 - HK...Nguyen Thanh Tu Collection
 
CapTechU Doctoral Presentation -March 2024 slides.pptx
CapTechU Doctoral Presentation -March 2024 slides.pptxCapTechU Doctoral Presentation -March 2024 slides.pptx
CapTechU Doctoral Presentation -March 2024 slides.pptxCapitolTechU
 
Work Experience for psp3 portfolio sasha
Work Experience for psp3 portfolio sashaWork Experience for psp3 portfolio sasha
Work Experience for psp3 portfolio sashasashalaycock03
 

Último (20)

P4C x ELT = P4ELT: Its Theoretical Background (Kanazawa, 2024 March).pdf
P4C x ELT = P4ELT: Its Theoretical Background (Kanazawa, 2024 March).pdfP4C x ELT = P4ELT: Its Theoretical Background (Kanazawa, 2024 March).pdf
P4C x ELT = P4ELT: Its Theoretical Background (Kanazawa, 2024 March).pdf
 
How to Manage Cross-Selling in Odoo 17 Sales
How to Manage Cross-Selling in Odoo 17 SalesHow to Manage Cross-Selling in Odoo 17 Sales
How to Manage Cross-Selling in Odoo 17 Sales
 
10 Topics For MBA Project Report [HR].pdf
10 Topics For MBA Project Report [HR].pdf10 Topics For MBA Project Report [HR].pdf
10 Topics For MBA Project Report [HR].pdf
 
ARTICULAR DISC OF TEMPOROMANDIBULAR JOINT
ARTICULAR DISC OF TEMPOROMANDIBULAR JOINTARTICULAR DISC OF TEMPOROMANDIBULAR JOINT
ARTICULAR DISC OF TEMPOROMANDIBULAR JOINT
 
Clinical Pharmacy Introduction to Clinical Pharmacy, Concept of clinical pptx
Clinical Pharmacy  Introduction to Clinical Pharmacy, Concept of clinical pptxClinical Pharmacy  Introduction to Clinical Pharmacy, Concept of clinical pptx
Clinical Pharmacy Introduction to Clinical Pharmacy, Concept of clinical pptx
 
Prescribed medication order and communication skills.pptx
Prescribed medication order and communication skills.pptxPrescribed medication order and communication skills.pptx
Prescribed medication order and communication skills.pptx
 
How to Show Error_Warning Messages in Odoo 17
How to Show Error_Warning Messages in Odoo 17How to Show Error_Warning Messages in Odoo 17
How to Show Error_Warning Messages in Odoo 17
 
How to Send Emails From Odoo 17 Using Code
How to Send Emails From Odoo 17 Using CodeHow to Send Emails From Odoo 17 Using Code
How to Send Emails From Odoo 17 Using Code
 
Ultra structure and life cycle of Plasmodium.pptx
Ultra structure and life cycle of Plasmodium.pptxUltra structure and life cycle of Plasmodium.pptx
Ultra structure and life cycle of Plasmodium.pptx
 
AUDIENCE THEORY -- FANDOM -- JENKINS.pptx
AUDIENCE THEORY -- FANDOM -- JENKINS.pptxAUDIENCE THEORY -- FANDOM -- JENKINS.pptx
AUDIENCE THEORY -- FANDOM -- JENKINS.pptx
 
How to Add Existing Field in One2Many Tree View in Odoo 17
How to Add Existing Field in One2Many Tree View in Odoo 17How to Add Existing Field in One2Many Tree View in Odoo 17
How to Add Existing Field in One2Many Tree View in Odoo 17
 
How to Make a Field read-only in Odoo 17
How to Make a Field read-only in Odoo 17How to Make a Field read-only in Odoo 17
How to Make a Field read-only in Odoo 17
 
The Stolen Bacillus by Herbert George Wells
The Stolen Bacillus by Herbert George WellsThe Stolen Bacillus by Herbert George Wells
The Stolen Bacillus by Herbert George Wells
 
Easter in the USA presentation by Chloe.
Easter in the USA presentation by Chloe.Easter in the USA presentation by Chloe.
Easter in the USA presentation by Chloe.
 
KARNAADA.pptx made by - saransh dwivedi ( SD ) - SHALAKYA TANTRA - ENT - 4...
KARNAADA.pptx  made by -  saransh dwivedi ( SD ) -  SHALAKYA TANTRA - ENT - 4...KARNAADA.pptx  made by -  saransh dwivedi ( SD ) -  SHALAKYA TANTRA - ENT - 4...
KARNAADA.pptx made by - saransh dwivedi ( SD ) - SHALAKYA TANTRA - ENT - 4...
 
3.26.24 Race, the Draft, and the Vietnam War.pptx
3.26.24 Race, the Draft, and the Vietnam War.pptx3.26.24 Race, the Draft, and the Vietnam War.pptx
3.26.24 Race, the Draft, and the Vietnam War.pptx
 
Drug Information Services- DIC and Sources.
Drug Information Services- DIC and Sources.Drug Information Services- DIC and Sources.
Drug Information Services- DIC and Sources.
 
CHUYÊN ĐỀ DẠY THÊM TIẾNG ANH LỚP 11 - GLOBAL SUCCESS - NĂM HỌC 2023-2024 - HK...
CHUYÊN ĐỀ DẠY THÊM TIẾNG ANH LỚP 11 - GLOBAL SUCCESS - NĂM HỌC 2023-2024 - HK...CHUYÊN ĐỀ DẠY THÊM TIẾNG ANH LỚP 11 - GLOBAL SUCCESS - NĂM HỌC 2023-2024 - HK...
CHUYÊN ĐỀ DẠY THÊM TIẾNG ANH LỚP 11 - GLOBAL SUCCESS - NĂM HỌC 2023-2024 - HK...
 
CapTechU Doctoral Presentation -March 2024 slides.pptx
CapTechU Doctoral Presentation -March 2024 slides.pptxCapTechU Doctoral Presentation -March 2024 slides.pptx
CapTechU Doctoral Presentation -March 2024 slides.pptx
 
Work Experience for psp3 portfolio sasha
Work Experience for psp3 portfolio sashaWork Experience for psp3 portfolio sasha
Work Experience for psp3 portfolio sasha
 

NetBioSIG2012 ugurdogrusoz-cbio

  • 1. Network Visualization and Analysis in the cBio Cancer Genomics Portal U. Dogrusoz, S.O. Sumer, S. Sonlu, J. Gao, B.A. Aksoy, B.E. Gross, N. Schultz, E. Cerami, C. Sander
  • 2. cBio Cancer Genomics Portal Goal: Make complex genomic data available through an intuitive interface Allow explorative data analysis / hypothesis testing / visualization Cerami et al. 2012, Cancer Discovery
  • 4. cBio Cancer Genomics Portal Cerami et al. 2012, Cancer Discovery
  • 6. Pathway Commons Cerami et al 2010, Nucl Acids Res
  • 8. Hairball Problem Complete network for TP53, MDM2, MDM4 & CDKN2A (463 interacting neighbors) This complete network can be downloaded in SIF or GraphML in cBio Portal.
  • 9. Pre-filtered network based on alteration frequencies The network below contains 54 nodes, including your 4 query genes and the 50 most frequently genes out 463 altered neighbor genes(out of 463). Query genes: CDKN2A MDM2 MDM4 TP53
  • 11. Genomic data overlaid on interaction network
  • 12. Genomic data overlaid on interaction network Alteration frequency: the % of samples that were altered on the gene
  • 13. Genomic data overlaid on interaction network Color gradient •white to red •based on alteration frequency Genomic data •mutation •copy number •mRNA expression
  • 14. Further filtering by genomic alterations Filter genes by alteration frequency Slide to threshold Or type value threshold value
  • 15. Further filtering by genomic alterations Gene with total alteration frequency 12% or less filtered out
  • 16. Filtering by genes of interest Hide selected genes from the network Search genes by name Select genes from canvas or gene list under Genes tab
  • 17. Filtering by interaction type & source Interactions Interactions merged by default Type (color-coded) & source shown in interaction details Shown individually
  • 18. Filtering by interaction type & source
  • 19. Filtering by interaction type & source
  • 20. Automatic network layout Change layout Recalculate options layout Recalculate layout after filtering
  • 21. Iterative network analysis Re-submit selected genes to the portal
  • 22. Drugs of New cBioPortal features specified genes Drug – gene targeting • Data source is DrugBank database of detail: Level (http://www.drugbank.ca) -None Inspect details targeting specified-FDA approved only • Only drugs genes shown including: -All -Targeted genes -Corresponding DrugBank page
  • 23. Other new cBioPortal features Network visualization service for IGV • Glioblastoma, RB pathway
  • 24. Other new cBioPortal features Cross-cancer query
  • 25. Other new cBioPortal features Oncoprint improvements Protein/phosphoprotein Mutation details event call
  • 26. Other new cBioPortal features Mutation diagram
  • 27. Other new cBioPortal features Many new cancer studies • 21 (5 of them published, rest provisional) cancer studies
  • 28. Work in progress and future plans • SBGN-compliant viewer (GSoC) – Networks presented in SBGN Process Description language • Construct Network-of-Interest from Genes-of- Interest using linker paths (Dogrusoz et al, 2009, BMC Bioinf) • Roundtrip analysis (query, modify, re-query, …) • Better/incremental layout • Use Cytoscape Web 2 (html5 version)
  • 29. Acknowledgements • Bilkent University • MSKCC – S. Onur Sumer – S. Onur Sumer – Sinan Sonlu – Jianjiong Gao – Naim Kucukdemirci – B. Arman Aksoy – Istemi Bahceci – Benjamin E. Gross – Nikolaus Schultz – Ethan Cerami – Chris Sander

Notas do Editor

  1. B) The RB Oncoprint, alterations of genes in this pathway tend to be mutually exclusiveC) Many RB1 mutations may have strong functional consequences as predicted by MutationAccessor.orgD) CDK4 mRNA expression is elevated in amplified casesE) Cases with an RB pathway alteration have worse overall survival than cases without an RB pathway alterationF) Network tab provides interactive analysis and visualization of networks altered in the chosen cancer study
  2. The network of interest built from genes of interest consists of pathways and interactions derived from the open-source Pathway Commons project.
  3. PC provides a central, convenient point of access to multiple publicly available pathway and interaction databases. It does so by integrating data sources formatted in the BioPAX or PSI–MI standards, and making all data sets available via a unified web site, a single web service interface and a batch download site.
  4. Glioblastoma: TP53 Pathway (4 genes)
  5. Links to IGV for visualization of DNA copy-number changes (through Web Start)
  6. Links to IGV for visualization of DNA copy-number changes (through Web Start)
  7. Cross-cancer functionality enables users to query across all cancer studies in our database
  8. OncoPrints are compact means of visualizing distinct genomic alterations, including somatic mutations, copy number alterations, and mRNA expression changes across a set of cases. They are extremely useful for visualizing gene set and pathway alterations across a set of cases, and for visually identifying trends, such as trends in mutual exclusivity or co-occurence between gene pairs within a gene set. Individual genes are represented as rows, and individual cases or patients are represented as columns.
  9. Mutation Diagrams show mutations in the context of protein domains.