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

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Presentation transcript:

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

Need for co-expression studies Measure of expression similarity Guilt-by-association: similarity in regulation, function When and where are genes expressed? Which genes show similar expression? Which known genes co-express with unknown genes? Spatial and temporal behavior of networks Dynamics of protein-protein interactions

Preprocessing of microarray data PREPROCESSING Raw microarray data Background correction Normalization Summarization Log2 absolute expression values

Co-expression High correlation coefficient Expression value Low correlation coefficient Gene A Gene B Gene A Gene C Pearson correlation coefficient: (range: -1,0,1)

Predefined microarray expression compendia  Compendium 1 (bias towards cell cycle, growth, development)  Compendium 2 (no bias, no redundancy in experiments)  AtGenExpress  Abiotic stress  Biotic stress  Stress (abiotic + biotic)  Hormone treatment  Genetic modification  Development  Flower  Leaf  Root  Seed  Whole plant User-defined microarray expression compendia  Compilation of public microarrays  Compilation of private microarrays  Compilation of public and private microarrays Multiple microarray expression compendia simultaneously

Expression compendia Leaf compendium Seed compendium Abiotic stress compendium Hormone compendium Co-expression in multiple datasets is important

Network exploration in Cytoscape Node and edge attribute browser Cytoscape LinkOut VizMapper

NODE ATTRIBUTES

LinkOut

CO-EXPRESSION EDGE ATTRIBUTES

PPI EDGE ATTRIBUTES

VIZMAPPER

Acknowledgements Stefanie De Bodt Jens Hollunder Nick Meulemeester Hilde Nelissen Thomas Van Parys Michiel Van Bel Klaas Vandepoele Yves Van de Peer Dirk Inzé Published version: De Bodt, S., Carvajal, D., Hollunder, J., Van den Cruyce, J., Movahedi, S., Inzé, D. (2010) CORNET: a user-friendly tool for data mining and integration. Plant Physiology

MicroarrayCORNET 1.0CORNET 2.0 Number of arrays3055 Number of experiments1209 Number of series200 Number of experiments with 2 replicates634 Number of experiments with more than 2 replicates575 Protein-protein interactions Vidal - Number of experimentally identified PPIs-6205 MIND0.5 – Number of experimentally identified PPIs Other – Number of experimentally identified PPIs Number of experimentally identified PPIs Number of computationally predicted PPIs Total number of PPIs Regulatory interactions Number of confirmed AGRIS interactions-574 Number of unconfirmed AGRIS interactions Number of gene-target relations (genetic_modification) Total number of regulatory interactions Gene-gene associations AraNet – Total number of associations CORNET statistics