© ETH Zürich | Genevestigator | This module was contributed by Philip Zimmermann Genevestigator...
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Transcript of © ETH Zürich | Genevestigator | This module was contributed by Philip Zimmermann Genevestigator...
![Page 1: © ETH Zürich | Genevestigator | This module was contributed by Philip Zimmermann Genevestigator – Module I Overview of Genevestigator.](https://reader036.fdocuments.us/reader036/viewer/2022062404/551b5cc55503465c7e8b606e/html5/thumbnails/1.jpg)
© ETH Zürich | Genevestigator | This module was contributed by Philip Zimmermann
Genevestigator – Module I
Overview of Genevestigator
![Page 3: © ETH Zürich | Genevestigator | This module was contributed by Philip Zimmermann Genevestigator – Module I Overview of Genevestigator.](https://reader036.fdocuments.us/reader036/viewer/2022062404/551b5cc55503465c7e8b606e/html5/thumbnails/3.jpg)
3Teaching modules Genevestigator® / ETH Zurich / [email protected]
Genevestigator Website
Start link for analysis tool (client java application)
User registration and/or subscription
User manual, FAQ
Teaching modules
Community pages
Publications
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4Teaching modules Genevestigator® / ETH Zurich / [email protected]
Database and application server
Expression measurement data (Affymetrix arrays)
Experiment and sample information (meta-data)
Data from mouse, rat, arabidopsis, barley
Metabolic and regulatory pathways
User management
MySQL database
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5Teaching modules Genevestigator® / ETH Zurich / [email protected]
Genevestigator client java application
Java tool - starts in browser
Four tool sets Meta-Profile Analysis
Biomarker Search
Clustering Analysis
Pathway Projector
Focus on the biological context
(anatomy, development, stimulus, mutation)
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6Teaching modules Genevestigator® / ETH Zurich / [email protected]
Genevestigator client java application
Minimal requirements: Java 1.4.2 or higher (working in browser)
128 MB RAM
Recommended: Screen resolution: 1024 x 768 or higher
500 MB RAM or more (for advanced tasks, e.g. you perform a
clustering analysis of many genes)
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7Teaching modules Genevestigator® / ETH Zurich / [email protected]
Quality control
Unprocessed probe intensity
Affymetrix QC metrics
RNA degradation plots
Probe-level analysis (RLE, NUSE)
Border element analysis
Array-array correlation plots
![Page 8: © ETH Zürich | Genevestigator | This module was contributed by Philip Zimmermann Genevestigator – Module I Overview of Genevestigator.](https://reader036.fdocuments.us/reader036/viewer/2022062404/551b5cc55503465c7e8b606e/html5/thumbnails/8.jpg)
8Teaching modules Genevestigator® / ETH Zurich / [email protected]
Tools & Products
Genevestigator® Advanced
Genevestigator® Classic
(Free for academic users)
(Small fee requested per academic laboratoryto support costs of development and curation)
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9Teaching modules Genevestigator® / ETH Zurich / [email protected]
Meta-Profile Analysis
Goal: study expression in given biological contexts
Tools: Selection (all signal values on screen; magnifying glass)
Northern (view signal values in a selected subset of arrays)
Anatomy (expression across anatomy categories)
Development (expression throughout development)
Stimulus (expression in response to stimuli or drugs)
Mutation (expression in response to genetic modifications)
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10Teaching modules Genevestigator® / ETH Zurich / [email protected]
Meta-Profile Analysis - screenshots
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11Teaching modules Genevestigator® / ETH Zurich / [email protected]
Biomarker Search
Goal: to identify genes that exhibit specific expression
Tools: Anatomy
Development
Stimulus
Mutation
Single or multiple target categories possible
„Supervised biclustering“
![Page 12: © ETH Zürich | Genevestigator | This module was contributed by Philip Zimmermann Genevestigator – Module I Overview of Genevestigator.](https://reader036.fdocuments.us/reader036/viewer/2022062404/551b5cc55503465c7e8b606e/html5/thumbnails/12.jpg)
12Teaching modules Genevestigator® / ETH Zurich / [email protected]
Biomarker Search - screenshots
Mouse development: markers forstage 4 or 5 (Theiler: 16 or 21)
Multiple targets or „supervised biclustering“
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13Teaching modules Genevestigator® / ETH Zurich / [email protected]
Clustering Analysis
Goal: identify groups of genes with similar expression
profiles
Tools: Hierarchical clustering (with leaf ordering)
Biclustering (BiMax algorithm)
Clustering of „raw“ gene expression or meta-profiles
(generate gene-array or gene-meta-profile matrix)
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14Teaching modules Genevestigator® / ETH Zurich / [email protected]
Clustering Analysis
Hierarchical clustering
Without leaf ordering
With leaf ordering
Biclustering
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15Teaching modules Genevestigator® / ETH Zurich / [email protected]
Pathway Projector
Goal: study the expression state or response of
metabolic and regulatory networks
Top-down or bottom-up analysis possible
Nodes = reactions
Edges = metabolites (met. map) or enzymes (reg. map)
Automatic layout, but often suboptimal: user can relocate
nodes and save view to file
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16Teaching modules Genevestigator® / ETH Zurich / [email protected]
Pathway Projector - screenshot
ABA response
Beta-alanine
Starch / sucrose
Inositolphosphate
Cold response
Phenylalanine / Tyrosine
Proline
ABA biosynthesis
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17Teaching modules Genevestigator® / ETH Zurich / [email protected]
Saving workspace
Goal: to allow a user to return to an analysis started
previously, or to share your analysis with colleagues
Workspace is saved to a file (*.gvw) and stores Array selections
Gene (probe set) selections
State of selections (marked/unmarked checkboxes)
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18Teaching modules Genevestigator® / ETH Zurich / [email protected]
Saving pathway views
Goal: to allow a user to build reaction networks and store
the layout and projected data
View is saved to a file (*.gvp) and stores: pathways involved
positions of nodes
data which is being projected (comparison set selections)
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19Teaching modules Genevestigator® / ETH Zurich / [email protected]
Exporting figures
Goal: to allow users to export high-quality, publish-ready
figures
Result views can be resized
and exported as: PNG
JPEG
EPS (for high resolution)
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20Teaching modules Genevestigator® / ETH Zurich / [email protected]
Summary of this module
Genevestigator has a website, a client Java application,
and several webservers.
The data is quality-controlled using Bioconductor and R
Two products (Classic and Advanced) are based on four
tool sets (Meta-Profile Analysis, Biomarker Search,
Clustering Analysis, Pathway Projector)
Saving workspaces and pathway views
Exporting figures