Transcript web-groups - Pathway Tools Software

Web Groups
&
Enrichment Analysis
Tim Holland
SRI Bioinformatics Research Group
June 2013
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Web Groups
• Groups are a powerful tool
• Collect lists of database objects
• Transform them into related objects
(eg: transform list of genes → list of pathways)
• Filter and analyze them in different ways
• Share with public or specific collaborators
• Visualize on cellular overview
• Export to spreadsheet, PortEco ClusterMyGenes
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Web Groups Location
• http://www.biocyc.org/groups
• To create Web Groups, you must first create a
(free) BioCyc account for yourself
• From the web menu: Tools → Groups
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Creating Groups: User-Defined Groups
• Create a group by uploading a tab-delimited text
file
• Groups -> New -> Group from Uploaded File
• Software will assist in recognizing database objects from
text
• Groups -> New -> Group from File of Replicon
Coordinates
• Regions with corresponding replicon database objects will
be created
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Creating Groups: User-Defined Groups
• Create a group by typing in names
Groups -> New -> Empty Group ; Add Row
• You will be presented with options for the correct object; e.g. typing
“tryptophan”, you will get the option to choose the compound L-tryptophan,
the enzyme tryptophan synthase, and others
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Creating Groups from Search Results
Turn into a group button appears on all search
results
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Using Groups: Group Transformations
Use Case: Find all genes that are regulated by a
transcriptional regulator.
Step 1: Create a group that contains the
transcription factor.
Step 2: In the “Transforms” menu, select
“Regulation – genes regulated by polypeptide,
complex, or RNA”.
A new column containing all genes regulated by the
transcription factor is generated.
This group can be further transformed, e.g. into
metabolic pathways.
The resulting lists can be exported.
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Using Groups: Attributes
Use Case: Find the chromosome positions of all genes
encoding enzymes of a pathway, sort by position. Find
regulators of those genes.
Step 1: Create a group that contains the pathway.
Step 2: In the “Transforms” menu, select “Genes of pathway”.
Step 3: Select gene column and select
• Groups > New > Group from column OR
• Click “+” at top of gene column
Step 4: Select “left-end-position” from “Add Property Column”
menu and add. Sort by position by clicking on arrow in
column header.
Step 5: Select “Direct regulators of gene” from “Add Transform
Column” menu.
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Genes of Aspartate Superpathway
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Transforms
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Genes, Sequences, Regions….
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Set Operations on Groups
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New Features
Reorganized, New Transformations
Transformations now grouped together, ex: Regulation
transforms
Binding sites upstream of genes, remove objects present in other
species PGDB
New “virtual properties”
DNA sequences, object frame IDs, etc.
Filter, Region Modification, Other Menus improved
Import from Replicon Coordinates
Export to PortEco
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Sequence virtual property
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Imported Replicon Coordinates -> Regions
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Group from Uploaded Tab-Delimited File
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More Detailed Region Manipulation
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PortEco gene clustering of E. coli genes
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Enrichment Analysis
* Statistical method to find classes of objects that have
more or less objects than would be expected by
chance
* Based on the Hypergeometric Distribution
* Can perform enrichment, depletion, or both
* Multiple ontologies can be used in Pathway Tools
* Multiple testing correction optional
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Enrichment Dialog
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Lab Exercise
1. Search for compounds that have 'glucose' in their
name
2. Turn into group
3. Enrichment Analysis → Compounds Enriched for
Pathways
4. Use defaults in Enrichment pop-up, click 'OK’
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Select ten most enriched pathways
Groups → New → From checked rows
Reactions of pathway
New group of reactions (green button on column)
Groups → Paint Data → On cellular overview
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