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Published byNoah Farmer Modified over 9 years ago
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Cellular Overview and Omics Viewer
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SRI International Bioinformatics The Cellular Overview Diagram A way to quickly visualize an organism’s metabolism Generated automatically by Pathway Tools Can be a static display or a dataset viewing tool
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SRI International Bioinformatics 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 l Anabolism on the left, catabolism on the right, energy in the middle l Gray backgrounds indicate more specific functional groups l Non-pathway reactions on far right Generally, pathways flow downward
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SRI International Bioinformatics Physical Location in the Overview Non-cytoplasmic proteins with known locations shown l In E. coli, that means periplasmic, cell and outer membrane l This includes proteins with no associated reaction Cytoplasmic proteins with enzymatic activities shown l Non-enzymatic cytoplasmic proteins left off to avoid clutter Compare the gram-positive B. anthracis l Note pathway holes visualized as gray lines Overview>Show/Hide Transport Links
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SRI International Bioinformatics 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: l Zoom l Pop up pathways l Indicate pathway connections (clear in overview menu) l More
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SRI International Bioinformatics Highlighting in the Overview Overview>Highlight>many options l Pathway by class (biosynthesis > all > select all) l Reactions > All without EC numbers (note second color) u Note all reaction options (many!) l 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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SRI International Bioinformatics Highlighting to Compare Organisms Look at shared or nonshared reactions Example – E. coli reactions shared with humans Example – switch to B. anthracis l Reactions not shared with (human and coli) l Set from Any to All l One way to think about drug targeting, e.g. Quick note – cross-species comparison from pathways l Go to this from individual pathway pages l Compares presence of pathway in question, and reactions of that pathway
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SRI International Bioinformatics The Omics Viewer An intuitive, visual display of large data sets Visualize any data that attaches numbers to genes, proteins or compounds l Proteomics, metabolomics, genomics Accepts tab-delimited and SAM datasets
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SRI International Bioinformatics Using the Omics Viewer Overview>Omics Viewer>Text File / SAM Output Single-time-point experiment l Choose display l Relative/absolute data l What kind of data? l Which column is the data in? (Object IDs must be in zero) Color schemes l Default (not standard between different datasets) l Others (see next slide)
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SRI International Bioinformatics Omics Viewer Output Data report l Total data rows l Data rows not shown l Data rows with invalid data l Color key Display options l Set maximum cutoff for default color scheme (e.g. 0.3) l Set manual color cutoffs (e.g. 0.3, 0.6, 0.9) l Both options let you compare different experiments
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SRI International Bioinformatics 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 l Thus, all time points / data sets comparable l A good way to standardize across experiments Can move between experiments/time points manually Can save as HTML
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