sri international bioinformatics 1 smarttables & enrichment analysis peter karp sri...
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SRI International Bioinformatics1
SmartTables&
Enrichment Analysis
Peter Karp
SRI Bioinformatics Research Group
September 2015
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SmartTables (formerly Web Groups)• Collect lists of database objects
• Genes, metabolites, pathways, sequence regions, …
• Transform them into related objects (eg: transform list of genes → list of pathways)
• Filter and combine
• Share with public or specific collaborators, publish
• Export to spreadsheet
• Omics analyses
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SmartTables Location
BioCyc.org, HumanCyc.org, EcoCyc.org…
• To create saved SmartTables, create a (free) BioCyc account for yourself
• From the web menu:
SmartTables->My SmartTables
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Three Types of SmartTables• Created by you
• Public
• Special
• Most SmartTables associated with a single PGDB
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Creating SmartTables: User-Defined SmartTables
• Create a SmartTable• Type in metabolite
names• From search
results• Upload a tab-
delimited text file
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Creating SmartTables: User-Defined SmartTables
• Create a SmartTable by typing in names
• Operations -> New -> SmartTable of Objects from Text Entry
• Names will be converted to rows of objects
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Creating SmartTables from Search Results
Turn into a SmartTable button appears on all search results
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Using SmartTables: Browsing Attributes
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SmartTable Columns
• Object ID
• Sort
• Hide
• Set display mode• First column: object ID vs common-name• Sequences
• Delete
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SmartTable Transformations
Create new columns that are computed from existing columns
Those columns can be converted to new SmartTables via "+"
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Using SmartTables: SmartTable Transformations
Use Case: Find all genes that are regulated by a transcriptional regulator.
Step 1: Create a SmartTable 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 SmartTable can be further transformed, e.g. into metabolic pathways.
The resulting lists can be exported.
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Using SmartTables: 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
• Operations > 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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Other Operations on SmartTables
Set union, intersection, difference among two SmartTables
Filter SmartTable rows to keep/reject all rows containing specified value or substring or regular expression
Share SmartTable with public or specified users
Freeze SmartTable for publication
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Genes, Sequences, Regions….
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Set Operations on SmartTables
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Alignment Viewer
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Frozen SmartTables
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Collapsible Columns, Select Rows By Number
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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 Exercise1. Search for compounds that have 'glucose' in their
name
2. Turn into SmartTable
3. Enrichment Analysis → Compounds Enriched for Pathways
4. Use defaults in Enrichment pop-up, click 'OK’
5. Select ten most enriched pathways
6. Operations → New → From checked rows
7. Reactions of pathway
8. New SmartTable of reactions (green button on column)
9. Operations → Paint Data → On cellular overview
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Lab Exercise1. Create a SmartTable containing all E. coli enzymes
with a molecular weight greater than 500; determine the map positions of the genes encoding those enzymes
2. Determine which enzymes in E. coli are heteromultimers
3. Create a SmartTable of metabolites and determine what metabolic pathways those metabolites are involved in
4. Export a SmartTable to a file
5. Share a SmartTable with the person next to you