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Network construction and exploration using CORNET and Cytoscape - Excercises

Network construction and exploration using CORNET and Cytoscape - Excercises. SPICY WORKSHOP Wageningen, March 8 th 2012 Stefanie De Bodt. CORNET. https://bioinformatics.psb.ugent.be/cornet Use Firefox Accept certificate Allow popups . Excercise 1a: Pairwise co-expression using CORNET.

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Network construction and exploration using CORNET and Cytoscape - Excercises

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  1. Network construction and exploration using CORNET and Cytoscape-Excercises SPICY WORKSHOP Wageningen, March 8th 2012 Stefanie De Bodt

  2. CORNET • https://bioinformatics.psb.ugent.be/cornet • Use Firefox • Accept certificate • Allow popups

  3. Excercise 1a: Pairwise co-expression using CORNET • 32 Arabidopsis input genes • all expression datasets • no PCC threshold • (returns PCC > 0.6 and PCC < -0.6 when selecting • multiple expression datasets)

  4. Solution Excercise 1a 31 nodes 131 edges

  5. Excercise 1b: Pairwise co-expression using CORNET • Integration of homology links to pepper genes • Import Network in Cytoscape • File > Import > Network from Table (Text/MS-Excel) • Wizard > Text file import options > Network import options: interaction “homolog”

  6. Excercise 1b: Pairwise co-expression using CORNET • Merge networksin Cytoscape • Plugins > Merge networks > Union • Color edges according to “interaction” to distinguish co-expression and homology links - Vizmapper: edge color, discrete mapping

  7. Solution Excercise 1b 86 nodes 70 edges

  8. Solution Excercise 1b 86 nodes 201 edges

  9. Solution Excercise 1b

  10. Excercise 2a: Co-expression neighborhood using CORNET • 32 Arabidopsis input genes • all expression datasets • PCC > 0.85, 5 neighbors

  11. Solution Excercise 2a 482 nodes 496 edges

  12. Excercise 2b: Clustering co-expression network using Cytoscape • MCODE plugin (using Fluff option) • Can you identifiy subnetworks or clusters of tightly co-expressed genes in the network? • http://baderlab.org/Software/MCODE/UsersManual

  13. Solution Excercise 2b

  14. Excercise 2c: Functional annotation of co-expression network using CORNET and Cytoscape • Node attributes (Gene Ontology, Plant Ontology, protein domain, localization) • BinGO plugin – GO overrepresentation analysis • Which functional classes are enriched? • Do you find the same functional classes when using the complete network or using subnetworks?

  15. Solution Excercise 2c

  16. Solution Excercise 2c

  17. Solution Excercise 2c

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