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Overviews, Omics Viewers,
and Object Groups
Introduction
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 Each
overview is a genome-scale diagram of
cellular machinery
 Cellular Overview
 Regulatory Overview
 Genome Overview
 Overviews
viewers
painted with omics data become omics
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The Cellular Overview Diagram
 Metabolic
pathways, transporters, other
membrane proteins, periplasmic proteins
 Generated
automatically by Pathway Tools
 Can
be a static display or a dataset viewing tool
 Can
be printed as a poster
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Organization of the Overview
 Lines
are reactions, nodes are biochemical
species (compounds, proteins)
 There’s a legend explaining symbols used
 Includes metabolic and transport reactions
 Pathways grouped functionally
 Anabolism on the left, catabolism on the right, energy in the
middle
 Gray backgrounds indicate more specific functional groups
 Non-pathway reactions on far right
 Generally, pathways flow downward
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Physical Location in the Overview
 Non-cytoplasmic
proteins with known locations
shown
 In E. coli, that means periplasmic, cell and outer membrane
 This includes proteins with no associated reaction
 Cytoplasmic proteins with enzymatic activities
shown
 Non-enzymatic cytoplasmic proteins left off to avoid clutter
 Compare the gram-positive B. anthracis
 Note pathway holes visualized as gray lines
 Overview>Show/Hide Transport Links
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Mousing Over in the Overview
 Mousing
over a gray backing tells you the
pathway class
 Mousing over a node gives compound name and
pathway
 Mousing over a line gives similar information
 Can click through from anything to the PGDB
 Can right-click to:
 Zoom
 Pop up pathways
 Indicate pathway connections (clear in overview menu)
 More
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Highlighting in the Overview
 Overview>Highlight>many
options
 Pathway by class (biosynthesis > all > select all)
 Reactions > All without EC numbers (note second color)

Note all reaction options (many!)
Reactions > By modulation
 Can clear highlighting at any time
 Can save highlighting to file for later use
 Can do Genes and Compounds as well
 Can pull information from a file, or from answer
list

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Highlighting to Compare Organisms
 Look
at shared or nonshared reactions
 Example – E. coli reactions shared with humans
 Example – switch to a second organism
 Reactions not shared with (human and coli)
 Set from Any to All
 One way to think about drug targeting, e.g.
 Quick note – cross-species comparison from
pathways
 Go to this from individual pathway pages
 Compares presence of pathway in question, and reactions of
that pathway
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The Genome Overview Diagram
 Shows
genes schematically, not to scale (unlike
Genome Browser)
 Shows
transcription units and direction of
transcription
 Shows
 Mouse
protein versus RNA coding status
over for gene name, product, pathway
participation, and intergenic spacing
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The Regulatory Overview Diagram
 Displays
the regulatory network for your
organism
 At
the moment, regulatory relationships are only
curated
 Rings
show regulatory status
 Inner – regulators only
 Middle – regulators that are also regulated
 Outer – regulated only
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Exposing Regulatory Relationships
a gene and right-click on it – will be
presented with options
 Pick
 Can
show direct and indirect regulators and
regulatees
 Display
 Can
options available in the menu
show just the interacting part of the network
The Omics Viewers
 Intuitive,
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visual displays of large data sets
 Visualize
any data that attaches numbers to
genes, proteins or compounds
 Proteomics, metabolomics, genomics
 Accepts
tab-delimited and SAM datasets
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Using the Omics Viewers
 Overview>Omics
Viewer>Text File / SAM Output
 Single-time-point experiment
 Choose display
 Relative/absolute data
 What kind of data?
 Which column is the data in? (Object IDs must be in zero)
 Color schemes
 Default (not standard between different datasets)
 Others (see next slide)
Omics Viewer Output
 Data
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report
 Total data rows
 Data rows not shown
 Data rows with invalid data
 Color key
 Display options
 Set maximum cutoff for default color scheme (e.g. 0.3)
 Set manual color cutoffs (e.g. 0.3, 0.6, 0.9)
 Both options let you compare different experiments
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Viewing Multiple Data Sets
 View
as an Animation
 Typically a time course, but does not have to be
 Need to tell Pathway Tools which columns to use
 Same output color / cutoff selections as single
experiment
 If you use automatic color scale, it’s set to the
maximum shift in the experiment
 Thus, all time points / data sets comparable
 A good way to standardize across experiments
 Can move between experiments/time points
manually
 Can save as HTML
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Object Groups
Object Groups
 Define
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and save groups of genes, metabolites,
pathways, etc
 Paint
groups onto overviews
 Combine groups
 Transform groups
 Perform enrichment analysis
 Desktop
mode only
Group Creation
 Groups
can contain one or more object types
 Add
current object to group
 Right-click on object
 Add
from answer list
 Add
from file
 Type
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in names of objects
Paint Group Onto Overview(s)
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Combine Groups
 Union
 Intersection
 Difference
 Exclusive-Or
 Can
be used to combine query results
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Transform Groups
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 Genes
-> All pathways containing those genes
 Genes -> All TFs that regulate those genes
 Compounds
-> All pathways containing them
Transformation Examples
 EcoCyc:
Create an empty group
 Add “superpathway of chorismate”
 Transform to genes of pathway
 Transform to regulators of gene
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Enrichment Analysis
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 Is
some group statistically enriched for members
of a set within a PGDB?
 Examples:
Is a group of genes enriched for genes in one or more
metabolic pathways?
 Is a group of metabolites enriched for membership in one or
more metabolic pathways?

Enrichment Analysis
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 P-values
reflect probability that presence of group
members would have occurred by chance
 Create
new group or replace old group
 Latter can cause you to lose your old group