pathway database pathway comparison expression viewer discovery
DESCRIPTION
Pathway Database Pathway Comparison Expression Viewer Discovery. Pankaj Jaiswal Oregon State University. Pathways. Pathway Home. Reference Pathway databases developed by collaborators. Developed by Gramene. Developed by Collaborators and mirrored at Gramene. Gramene Pathway Navigation. - PowerPoint PPT PresentationTRANSCRIPT
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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Light LightDark Dark
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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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