Transcript ppt - PLEXdb

www.plexdb.org
Data Mining at
PLEXdb : Plant and
Plant Pathogen Gene
Expression Database
www.plexdb.org
Sudhansu Dash1,2,3, Hong Lu5, Ethalinda KS
Cannon3,5, Nick Lauter3,4, Volker Brendel5,
Roger P Wise4, Julie A Dickerson1,2
1Virtual
Reality Application Center; 2Dept. of
Electrical & Computer Engg.; 3Crop Genome
Informatics Lab; 4Dept. of Plant Pathology and
Corn Insects and Crop Genetics Research,
USDA-ARS; 5GDCB. Iowa State University.
PLEXdb Features:
• Supports all Affymetrix microarrays for plants and plant
pathogens including annotation.
• MIAME/Plant compliant data submission.
• Experiment Visibility: private / collaborators and
reviewers / public.
• Uses standard ontologies.
• Links to PlantGDB, Gramene, GrainGenes, UniProt, etc.
• Option to submit data at NCBI GEO
• Data from 217 microarray experiments, > 6000 chips
• Experiments from 14 Affymetrix arrays.
• Species: Arabidopsis, Barley, Citrus, Fusarium, Grape,
Maize, Medicago, Poplar, Rice, Soybean, Sugarcane,
Tomato, Wheat.
DATA MINING: The Microarray Platform Translator tool
Translates probe sets of one microarray chip to another in a different
species.
DATA MINING: Gene OScilloScope
Search for experiments where expression of queried genes fluctuate (oscillate) the
most.
DATA MINING: Find co-expressed genes
Co-expressed genes or profile
neighbors can be downloaded
and viewed as heatmap or
expression graph
GENELIST SUITE: Tools to Create GeneLists
GO category
Treatment specific expression
Fold change
GENELIST SUITE: Analyze GeneLists
Partitional clustering based on K Means
GENELIST SUITE: Annotate a GeneList
TOOLS: Map Interesting Genes from Your Analysis on
the rice/Arabidopsis Genome
Model Genome Interrogator
Get the gene model,
promoter, 5’UTR
sequences, etc.
VISUALIZATION: Emphasis on data exploration
VISUALIZATION:
Expression of an individual gene
Expression Graph of
probe set
OsAffx.26001.3.S1_at in
experiment OS2
across hybridizations:
Repressed in salt
stress condition.
CONTROL
SALT STRESS