SRI International Bioinformatics 1 SmartTables & Enrichment Analysis Peter Karp SRI...

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