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

Pathway DatabasePathway Comparison

Expression ViewerDiscovery.

Pankaj JaiswalOregon State University

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Pathways

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Pathway Home

Developed by Gramene

Developed by Collaborators and mirrored at Gramene

Reference Pathway databases developed by collaborators

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Gramene Pathway Navigation

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Pathway Browse Options

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Search Options and Selecting the Database

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Search Example and Pathway Views

Metabolites and small moleculesMetabolites and small molecules

EnzymeEnzyme

Gene productGene product

Downstream pathways

Downstream pathways

Zoom upto chemical

structures

Zoom upto chemical

structures

EvidenceEvidence

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Pathway ComparisonClick to visit

pathwayClick to visit

pathway

Click to visit the reaction

Click to visit the reaction

Click to visit the gene product

Click to visit the gene product

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Discovery Environment: Pathway comparison

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Cases with homologs not sharing the same Pathway

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Rice KS8 Vs Ath KS1

http://www.ncbi.nlm.nih.gov/pubmed/12805613?dopt=Abstract (Fleet etal 2003.)

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Beyond Pathway Views and Comparison !

Can I analyze my data live using the Pathway views?

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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)

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OMICs Viewer: The Expression Viewer

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Your sample file with expression data(tab delimited text/data file)

Columns:0 1 2 3 4 5 6 7 8 9 10 11 12

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/ID15

OMICs Viewer

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Expression view on the cellular overview

View data fromSingle data columnOR Data from multiple experiments/timeline/-columns

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Expression views in Pathway tool and database (local installation)

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From Pathway to Gramene’ Shopping Cart (GrameneMart) !

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Gramene

An Alliance for Plant Biologists and Online Resources

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We value your contribution and feedback.

Help us improve, innovate and

integrate.

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From Pathway to Gramene’ Shopping Cart (GrameneMart) !

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