1. Overviews, Omics Viewers, and Object Groups

2. SRI International Bioinformatics Introduction Each overview is a genome-scale diagram of cellular machinery l Cellular Overview l Regulatory Overview l Genome Overview Overviews painted with omics data become omics viewers

3. SRI International Bioinformatics 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

4. 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

5. 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

6. 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

7. 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

8. SRI International Bioinformatics Highlighting to Compare Organisms Look at shared or nonshared reactions Example – E. coli reactions shared with humans Example – switch to a second organism 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

9. SRI International Bioinformatics The 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

10. SRI International Bioinformatics The Regulatory Overview Diagram Displays the regulatory network for your organism At the moment, regulatory relationships are only curated Rings show regulatory status l Inner – regulators only l Middle – regulators that are also regulated l Outer – regulated only

11. SRI International Bioinformatics Exposing 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

12. SRI International Bioinformatics The Omics Viewers Intuitive, visual displays 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

13. SRI International Bioinformatics Using the Omics Viewers 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)

14. 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

15. 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

16. SRI International Bioinformatics Object Groups

17. SRI International Bioinformatics Object Groups Define and save groups of genes, metabolites, pathways, etc Paint groups onto overviews Combine groups Transform groups Perform enrichment analysis Desktop mode only

18. SRI International Bioinformatics 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 in names of objects

19. SRI International Bioinformatics Paint Group Onto Overview(s)

20. SRI International Bioinformatics Combine Groups Union Intersection Difference Exclusive-Or Can be used to combine query results

21. SRI International Bioinformatics Transform Groups Genes -> All pathways containing those genes Genes -> All TFs that regulate those genes Compounds -> All pathways containing them

22. SRI International Bioinformatics Transformation Examples EcoCyc: Create an empty group l Add “superpathway of chorismate” l Transform to genes of pathway l Transform to regulators of gene

23. SRI International Bioinformatics Enrichment Analysis Is some group statistically enriched for members of a set within a PGDB? Examples: l Is a group of genes enriched for genes in one or more metabolic pathways? l Is a group of metabolites enriched for membership in one or more metabolic pathways?

24. SRI International Bioinformatics Enrichment Analysis 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