Pathway Database Pathway Comparison Expression Viewer Discovery. Pankaj Jaiswal Oregon State University 1.

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Presentation transcript:

Pathway Database Pathway Comparison Expression Viewer Discovery. Pankaj Jaiswal Oregon State University 1

Pathways 2

Pathway Home Developed by Gramene Developed by Collaborators and mirrored at Gramene Reference Pathway databases developed by collaborators 3

Gramene Pathway Navigation 4

Pathway Browse Options 5

Search Options and Selecting the Database 6

Search Example and Pathway Views Metabolites and small molecules Enzyme Gene product Downstream pathways Zoom upto chemical structures Evidence 7

Pathway Comparison Click to visit pathway Click to visit the reaction Click to visit the gene product 8

Discovery Environment: Pathway comparison 9

Cases with homologs not sharing the same Pathway 10

Rice KS8 Vs Ath KS1 bmed/ ?dopt=Abstract bmed/ ?dopt=Abstract (Fleet etal 2003.) 11

Beyond Pathway Views and Comparison ! Can I analyze my data live using the Pathway views? 12

Transcriptome Data Hierarchical clustering of Arabidopsis cycling genes mapping to metabolic pathways (1753 genes). Mean centered expression levels are represented with green denoting down regulation, and red indicating upregulation. (Filichkin et al 2011 PLoS One June 2011) Light Dark 13

OMICs Viewer: The Expression Viewer 14

Your sample file with expression data (tab delimited text/data file) Columns: Gene/locus IDs (preferred) can be replaced by gene symbols and synonyms If the data is from metabolomics, these IDs in column-0 is replaced with the compound name/ID 15

OMICs Viewer 16

Expression view on the cellular overview View data from Single data column OR Data from multiple experiments/timeline/- columns 17

Expression views in Pathway tool and database (local installation) 18

From Pathway to Gramene’ Shopping Cart (GrameneMart) ! 19

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Gramene An Alliance for Plant Biologists and Online Resources 21

We value your contribution and feedback. Help us improve, innovate and integrate. 22

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From Pathway to Gramene’ Shopping Cart (GrameneMart) ! 24