Overviews and Omics Viewers

SRI InternationalBioinformaticsIntroduction

Each overview is a genome-scale diagram of a different aspect of the 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

Desktop vs Web version: Desktop has more commands currently Web version can be faster to zoom

SRI InternationalBioinformaticsOrganization of the

Cellular 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 gray background identifies pathway class

Mousing over a node gives compound name and pathway

Mousing over a line gives reaction informationCan click through from anything to the PGDB

SRI InternationalBioinformaticsZooming and Panning

Web mode: Hold mouse and drag to pan Click ladder at upper left, or double-click to zoom

Desktop: right-click to Zoom Pop up pathways Indicate pathway connections (clear in overview menu) More

SRI InternationalBioinformaticsHighlighting in the Overview

Desktop Mode

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 in the Overview

Web Mode

Cellular Overview>Highlight>many optionsClear/enable individual highlights using switching

panel at upper rightCan save highlighting to file for later useMultiple highlight

Highlight/Omics View Based on Names and Frame IDs

Generate URL that will re-create current highlighting pattern

Cellular Overview>Generate Bookmark for Current …

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Highlighting to Compare OrganismsDesktop ModeLook 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 InternationalBioinformaticsGenome Overview

To enter (desktop mode): Overviews > Show Genome Overview Genome Browser: Click level 4 (Genome)

To enter (web mode): Tools > Genome Overview Genome Browser: Click level 4 (Genome)

Mouse over genes for more informationDesktop: Substring search available

SRI InternationalBioinformaticsRegulatory Overview

Displays the regulatory network for an organism

At the moment, regulatory relationships must curated or loaded from an external database

Rings show regulatory status Inner – regulators only Middle – regulators that are also regulated Outer – regulated only

Desktop: Overviews > Show Regulatory OverviewWeb: Tools > Regulatory Overview

SRI InternationalBioinformaticsExploring Regulatory

Relationships

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

Highlight genes by GO terms or substring

Can show direct and indirect regulators and regulatees

Display options available in the menu Change layout Display highlighted genes only Zoom and pan

SRI InternationalBioinformaticsAnalysis of Omics Datasets

Omics Viewers Cellular Overview Regulatory Overview Genome Overview

Genome Browser tracks

Groups facility Define groups of differentially regulated genes Perform enrichment analysis Transform to operons Transform to significantly expressed pathways

SRI InternationalBioinformaticsThe Omics Viewers

Intuitive, visual displays of large data sets using the three overviews

Visualize any data that attaches numbers to genes, proteins or compounds

Proteomics, metabolomics, genomics

Accept tab-delimited and SAM (desktop only) datasets

Some differences between desktop and web versions

Omics pop-ups are desktop only

SRI InternationalBioinformaticsUsing the Omics Viewers

Entry Desktop: Overview>Omics Viewer>Text File / SAM Output Web: Cellular Overview > Highlight Experimental Data

Single-time-point experiment Choose which omics viewers to use

Data file Object IDs must be in column zero What object IDs to use? Which column is the data in? Labels can be specified in the data file in first non-comment

line: $Label1 Label2 Label3

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 InternationalBioinformaticsOmics Viewer Options

Relative vs absolute Absolute: Concentrations or molecule counts. Negative

values are ignored. Relative: Assumes values are centered

0-centered vs 1-centered scale 0-centered = log scale with positive and negative values 1-centered = linear scale, centered on 1, log transform

SRI InternationalBioinformaticsOmics Viewer Color Schemes

Full color spectrum from data Data from one file mapped to full color spectrum Different experiments will receive different color assignments

Full color spectrum with max cutoff User specifies cutoff Useful for comparing datasets

Three color display with threshold Three color bins: x < 1/T , 1/T < x < T, x > T

User-defined bins with computer colorsUser-defined bins with user colors

SRI InternationalBioinformaticsViewing Multiple Data Sets

Compare multiple data points using 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 InternationalBioinformaticsOmics Pop-Ups

Desktop only for now; web versions to come

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Omics Data Graphing on Cellular Overview

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SRI InternationalBioinformaticsUsing Groups for Omics

Data Analysis

Define group from omics data file

Enrichment analysis

Groups Transform Group Pathways of Gene Significant Pathways of Gene Genes in Same Operon Regulators of Gene Enrichment Analysis