Transcript ExPlainTraining

Introduction to
ExPlain™
What is ExPlain?
ExPlain is a set of tools for the analysis of
gene sets and sequences
It can be used to:
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Find binding sites in a promoter
Build composite binding site models
Map gene and protein lists to pathways
Explore and view gene regulatory networks
ExPlain Tools
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Classification into functional categories (GO, diseases, tissues)...
Enrichment analysis...
Mapping on canonical pathways...
Mapping on user interaction pathways...
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TF binding site search (Match)...
Combined pattern and matrix search (PMatch)...
CM: Composite Models (genetic algorithm)...
Identify Composite Model regulated genes...
Phylogenetic footprinting (conserved TFBS)...
Filter sites using intervals...
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Search for key nodes...
Search for clusters...
Regulatory
Network Analysis
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Statistics calculator...
Generate graph on interval...
Generate graph on geneset...
Graphing Widgets
Mapping to known
pathways
Binding Site
Analysis
The ExPlain Interface
File Menu
Data Menu
Analysis Menu
Icons and Tools
Context Specific
The Wizards
Wizards - Automated work flows for common
analyses
4 separate workflows
A good place to start
Wizard as a Reminder
Binding Site Analysis
• Binding Site
Representation as a
matrix
• Each site has a
specificity
• These are created
from experimental
evidence
Match uses these matrices to find
new potential binding sites
MATCH Parameters
Promoters to Analyze
Set to compare to
Matrixes to use
Note on loading sequences
Promoter window
TSS
Sequence
5’
-1000
Default promoter
position
0
100
3’
Composite Models
• Create combinations of binding sites that
are unique to a gene set.
• This input for a composite model search in
a gene set and a MATCH output.
Key Node Analysis
• Find nodes that are connected to gene in
network.
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Gene1
Gene2
Gene3
Cluster Analysis
• Tries to connect each pair of molecules of
the input set.
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Gene3
Gene1
Gene2
Exercises for Today
1. Find binding sites on a sequence
2. Pathway Analysis
– Map a gene set to pathway
– Enrichment Analysis
3. Find over and under represented binding
sites in a gene set
4. Construct a composite model
5. Find key node
6. Use the viewer