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GENEVESTIGATOR
Overview of Genevestigator
Content
Introduction
Tools
Metaprofile analysis
Biomarker search
RefGenes
Clustering analysis
Additional tips
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Concept of Genevestigator
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Tissue type 1Tissue type 2Tissue type 3Tissue type 4………Tissue type 200
Thousands of microarrayexperiments world-wide
Curation of data and annotation
Model of a summarized output
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Curation: normalization and annotation of- Anatomy- Development- Stimulus and Mutation
Establishment of the
Genevestigator Database
Curation: quality control of microarray data
Unprocessed probe intensity
RNA degradation plots
Probe-level analysis (RLE, NUSE)
Border element analysis
Array-array correlation plots
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Overview of the Genevestigator System
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Database and Application Server Cluster
Website Java Client Application
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GENEVESTIGATOR
Tools
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Genevestigator CLASSIC tool: Meta Profile Analysis
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Meta Profile Analysis: analytical approach
genes
Anatomy[space]
Development[time]
Stimulus /Mutation[response]
which conditions?
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Meta-Profile Analysis
1. Chose an organism
2. Enter the genes you wish to work with
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Meta-Profile Analysis
View and interpret the results across:– Anatomical categories (Anatomy tab)– Developmental stages (Development tab)– Chemicals, diseases, treatments, etc. (Stimulus tab)– Genetic modifications (Mutation tab)– Tumor types (Neoplasm tab)
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Meta-Profile Analysis: Anatomy tool
Looks at how genes are expressed in different tissues
Mean and standard deviation
Anatomy categories as a tree (ontology); expand / collapse
Number of arrays per category is indicated
Anatomical expression profile of ß-Actin in the mouse
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Meta-Profile Analysis: Development tool
Looks at how genes are expressed during the life cycle of an organism
Example for human
Example for mouse / rat
Expression profile of BDNF across the human development
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Meta-Profile Analysis: Stimulus and Mutation tools
List (or tree)of variousconditions
Most upregulating conditions
Most downregulating conditions
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Meta-Profile Analysis: Neoplasm tool
Looks at how genes are expressed in different tumors
Mean and standard error
Tumors ordered as a tree (ontology); expand / collapse
Number of arrays per category is indicated
Expression profile of NPY1 receptor across human tumors
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Genevestigator ADVANCED Tools
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Biomarker search: analytical approach
Anatomy[space]
Development[time]
Stimulus /Mutation[response]
conditions which genes?
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Biomarker search
1. Chose an organism
3. Save target genes for further analysis
2. Chose conditions and run analysis
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Biomarker Search
Identify genes that exhibit specific expression characteristics
Anatomy
Development
Stimulus / Mutation
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Biomarker Search in Genevestigatorco
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gene 1
gene 2
gene 3
gene 4
gene 5
gene 6
gene 7
gene 8
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gene 10
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gene 13
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gene 16
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target condition
other conditions to which the genes are responding
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Biomarker Search in Genevestigator
Example: human genes responsive to Actinomycin-D
Actinomycin-D
Cell cycle inhibition
Echinomycin
Chemical: ARC
SapphyrinPropiconazoleOncolytic herpessimplex virus
vMyb
target condition(s)
co-inducing conditions
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RefGenes – find the best housekeeping genes
Validation experimenton mouse liver
geNorm selection of the moststable reference genes within
this experiment
Dataset: 197 arrays from mouse liver
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Clustering Analysis
Goal: to identify groups of genes that have similar expression characteristics
Tools:– Hierarchical clustering (with leaf
ordering)– Biclustering (BiMax algorithm)
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Hierarchical clustering
Cluster sets of genes expressed at different stages of plant development
HC using leaf ordering algorithm
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Biclustering
Search for biclusters in a list of 64 genes responsive to myocardial infarction
One of many possible biclusters Development profile of these 7 genes
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GENEVESTIGATOR
Useful features
Tooltips (mouse-over) provide detailed information abouta treatment, a spot, or an experiment.
Useful features - tooltips
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Focus function
Note: be sure that genes and organism/arrays are compatible! (e.g. you cannot look at mouse genes in a selection of rat arrays…)
Focus on an array selection
Focus on a gene selection
tools will compile results from this combination of data
allows to easily jump from one selection of genes or arrays to another selection
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Exporting figures
scale export image
Save export image in:• PNG• JPEG• EPS
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Exporting data
Export content:
• Mean value• Standard error values
Export format:
• tab-delimited (TXT) or• comma-separated (CSV)
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Saving workspaces
Saves content of selections:
• selections of experiments and arrays
• selections of genes• status of checkboxes
• Benefits: • allows to share results
between colleagues• allows to continue your
research at a later stage without losing the context
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GENEVESTIGATOR
End of presentation
