Overviews, Omics Viewers,and Object Groups

SRI InternationalBioinformaticsIntroduction

Each overview is a genome-scale diagram of cellular machinery

Cellular Overview Regulatory Overview Genome Overview

Overviews painted with omics data become omics viewers

SRI InternationalBioinformaticsThe 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

SRI InternationalBioinformaticsOrganization of the Overview

Lines are reactions, nodes are biochemical species (compounds, proteins)

There’s a legend explaining symbols usedIncludes metabolic and transport reactionsPathways 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

SRI InternationalBioinformaticsPhysical 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 clutterCompare the gram-positive B. anthracis

Note pathway holes visualized as gray linesOverview>Show/Hide Transport Links

SRI InternationalBioinformaticsMousing 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 informationCan click through from anything to the PGDBCan right-click to:

Zoom Pop up pathways Indicate pathway connections (clear in overview menu) More

SRI InternationalBioinformaticsHighlighting 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 timeCan save highlighting to file for later useCan do Genes and Compounds as wellCan pull information from a file, or from answer

list

SRI InternationalBioinformaticsHighlighting to Compare

Organisms

Look at shared or nonshared reactionsExample – E. coli reactions shared with humansExample – 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

SRI InternationalBioinformaticsThe Genome Overview Diagram

Shows genes schematically, not to scale (unlike Genome Browser)

Shows transcription units and direction of transcription

Shows protein versus RNA coding status

Mouse over for gene name, product, pathway participation, and intergenic spacing

SRI InternationalBioinformaticsThe 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

SRI InternationalBioinformaticsExposing Regulatory

Relationships

Pick a gene and right-click on it – will be presented with options

Can show direct and indirect regulators and regulatees

Display options available in the menu

Can show just the interacting part of the network

SRI InternationalBioinformaticsThe Omics Viewers

Intuitive, 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

SRI InternationalBioinformaticsUsing the Omics Viewers

Overview>Omics Viewer>Text File / SAM OutputSingle-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)

SRI InternationalBioinformaticsOmics Viewer Output

Data 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

SRI InternationalBioinformaticsViewing Multiple Data Sets

View as an AnimationTypically a time course, but does not have to beNeed to tell Pathway Tools which columns to useSame output color / cutoff selections as single

experimentIf 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

SRI InternationalBioinformatics

Object Groups

SRI InternationalBioinformaticsObject Groups

Define and save groups of genes, metabolites, pathways, etc

Paint groups onto overviewsCombine groupsTransform groupsPerform enrichment analysis

Desktop mode only

SRI InternationalBioinformaticsGroup Creation

Groups can contain one or more object types

Add current object to groupRight-click on object

Add from answer list

Add from file

Type in names of objects

SRI InternationalBioinformaticsPaint Group Onto Overview(s)

SRI InternationalBioinformaticsCombine Groups

UnionIntersectionDifferenceExclusive-Or

Can be used to combine query results

SRI InternationalBioinformaticsTransform Groups

Genes -> All pathways containing those genesGenes -> All TFs that regulate those genes

Compounds -> All pathways containing them

SRI InternationalBioinformaticsTransformation Examples

EcoCyc: Create an empty group Add “superpathway of chorismate” Transform to genes of pathway Transform to regulators of gene

SRI InternationalBioinformaticsEnrichment Analysis

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?

SRI InternationalBioinformaticsEnrichment Analysis

P-values reflect probability that presence of group members would have occurred by chance

Create new group or replace old groupLatter can cause you to lose your old group