Cellular Overview and Omics Viewer

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Cellular Overview and Omics Viewer
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The Cellular Overview Diagram

• A way to quickly visualize an organisms
  metabolism
• Generated automatically by Pathway Tools
• Can be a static display or a dataset viewing tool

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Organization of the Overview

• Lines are reactions, nodes are biochemical
  species (compounds, proteins)
• Theres 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
• OverviewgtShow/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

• OverviewgtHighlightgtmany options
• Pathway by class (biosynthesis gt all gt select
  all)
• Reactions gt All without EC numbers (note second
  color)
• Note all reaction options (many!)
• Reactions gt 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 B. anthracis
• 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 Omics Viewer

• An intuitive, visual display 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 Viewer

• OverviewgtOmics ViewergtText 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)

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Omics 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

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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, its 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