1. Overviews and Omics Viewers

2. SRI International Bioinformatics Introduction Each overview is a genome-scale diagram of a different aspect of the 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 Desktop vs Web version: l Desktop has more commands currently l Web version can be faster to zoom

4. SRI International Bioinformatics Organization of the Cellular 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 gray background identifies pathway class Mousing over a node gives compound name and pathway Mousing over a line gives reaction information Can click through from anything to the PGDB

7. SRI International Bioinformatics Zooming and Panning Web mode: l Hold mouse and drag to pan l Click ladder at upper left, or double-click to zoom Desktop: right-click to l Zoom l Pop up pathways l Indicate pathway connections (clear in overview menu) l More

8. SRI International Bioinformatics Highlighting in the Overview Desktop Mode 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

9. SRI International Bioinformatics Highlighting in the Overview Web Mode Cellular Overview>Highlight>many options Clear/enable individual highlights using switching panel at upper right Can save highlighting to file for later use Multiple highlight l Highlight/Omics View Based on Names and Frame IDs Generate URL that will re-create current highlighting pattern l Cellular Overview>Generate Bookmark for Current …

10. SRI International Bioinformatics Highlighting to Compare Organisms Desktop Mode 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

11. 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

12. SRI International Bioinformatics Genome Overview To enter (desktop mode): l Overviews > Show Genome Overview l Genome Browser: Click level 4 (Genome) To enter (web mode): l Tools > Genome Overview l Genome Browser: Click level 4 (Genome) Mouse over genes for more information Desktop: Substring search available

13. SRI International Bioinformatics Regulatory 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 l Inner – regulators only l Middle – regulators that are also regulated l Outer – regulated only Desktop: Overviews > Show Regulatory Overview Web: Tools > Regulatory Overview

14. SRI International Bioinformatics Exploring Regulatory Relationships Pick a gene and right-click on it – will be presented with options l Highlight genes by GO terms or substring Can show direct and indirect regulators and regulatees Display options available in the menu l Change layout l Display highlighted genes only l Zoom and pan

15. SRI International Bioinformatics Analysis of Omics Datasets Omics Viewers l Cellular Overview l Regulatory Overview l Genome Overview Genome Browser tracks Groups facility l Define groups of differentially regulated genes l Perform enrichment analysis l Transform to operons l Transform to significantly expressed pathways

16. SRI International Bioinformatics The Omics Viewers Intuitive, visual displays of large data sets using the three overviews Visualize any data that attaches numbers to genes, proteins or compounds l Proteomics, metabolomics, genomics Accept tab-delimited and SAM (desktop only) datasets Some differences between desktop and web versions l Omics pop-ups are desktop only

17. SRI International Bioinformatics Using the Omics Viewers Entry l Desktop: Overview>Omics Viewer>Text File / SAM Output l Web: Cellular Overview > Highlight Experimental Data Single-time-point experiment l Choose which omics viewers to use Data file l Object IDs must be in column zero l What object IDs to use? l Which column is the data in? l Labels can be specified in the data file in first non-comment line: u $Label1 Label2 Label3

18. 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

19. SRI International Bioinformatics Omics Viewer Options Relative vs absolute l Absolute: Concentrations or molecule counts. Negative values are ignored. l Relative: Assumes values are centered 0-centered vs 1-centered scale l 0-centered = log scale with positive and negative values l 1-centered = linear scale, centered on 1, log transform

20. SRI International Bioinformatics Omics Viewer Color Schemes Full color spectrum from data l Data from one file mapped to full color spectrum l Different experiments will receive different color assignments Full color spectrum with max cutoff l User specifies cutoff l Useful for comparing datasets Three color display with threshold l Three color bins: x T User-defined bins with computer colors User-defined bins with user colors

21. SRI International Bioinformatics Viewing Multiple Data Sets Compare multiple data points using 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

22. SRI International Bioinformatics Omics Pop-Ups Desktop only for now; web versions to come

23. SRI International Bioinformatics Omics Data Graphing on Cellular Overview

24. SRI International Bioinformatics

25. SRI International Bioinformatics Using Groups for Omics Data Analysis Define group from omics data file Enrichment analysis Groups  Transform Group  l Pathways of Gene l Significant Pathways of Gene l Genes in Same Operon l Regulators of Gene l Enrichment Analysis