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The Pathway/Genome Navigator

The Pathway/Genome Navigator provides comprehensive tools for managing and analyzing biological data. It allows users to query various data types, including genes, proteins, and pathways, through both direct and complex search strategies. The desktop version offers enhanced speed and capabilities, including PGDB creation and advanced omics analysis. Users can customize preferences, save favorite organisms, and receive updates. The Navigator supports both web and desktop modes, making it versatile for a range of research needs. Explore the Navigator's features and enhance your research today!

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The Pathway/Genome Navigator

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  1. The Pathway/Genome Navigator

  2. Overview • Data page types • General query strategies • Web queries • Desktop Pathway Tools • User preferences • Lab exercises

  3. Pathway/Genome Navigator • Navigator runs both on the desktop and on the web • Desktop version • Runs faster • More capabilities • PGDB creation, editing • Reachability analysis, metabolite tracing, object groups • More omics analysis • Both have capabilities the other does not have • http://biocyc.org/desktop-vs-web-mode.shtml

  4. Data Page Types for Individual PGDB Objects • Genes* • RNAs * • Proteins * • Enzymes, transporters, transcription factors, others • Extensive comments and citations • Monomers and multimers are represented, and in different chemical states • Transcription units • Reactions • Pathways • Compounds • Organisms • Searches are organized around these page types * Note: Gene pages will be merged with RNA and Protein pages in early 2010

  5. Direct Queries • Search for a specific object you know • Searches common to all object types • By name – must be exact (though there are synonyms) • By identifier • BioCyc ID • Accession number • Web only: UniProt ID • By substring – if you don’t know an exact name • Searches that are specific to object type

  6. Indirect Queries • Find an object by searching for an object that is probably related to it • Then navigate to the object you seek

  7. Complex Queries • Define multi-criteria searches • System returns all objects that meet those criteria

  8. BioCyc Web Site • Web browsers • Firefox • Safari • Chrome • Internet Explorer not recommended • Create a Web account • Save page formatting preferences, omics viewer preferences • Save default organism • Save organism lists for comparative analyses • Receive email updates on new releases

  9. Web Searches • Multiple searches available for finding information in different ways • Quick search (simplest search) • Object-specific searches • Ontology-based searches • Advanced search • http://biocyc.org/query.html • Searches of full-text literature articles

  10. Select Current Organism • Click on “change” • Under Quick Search button • Bottom of Search menu • Bottom of Tools menu • Select by typing or clicking

  11. Organism Pages • Tools -> Reports -> Summary statistics • PGDB authors, statistics

  12. Sample Web Searches for EcoCyc • Quick Search: xyl • Quick Search: trpa type:gene • Quick Search: b1200 • Search -> Genes/Proteins/RNAs • 40 < MW < 50 and 5.5 < pI < 6.0 • 3000000 < Map-Position < 3500000 and Has Gene Ontology term “locomotion” (under Biological Process)

  13. Sample Web Searches for HumanCyc • Quick Search: dopamine • Quick Search: dopamine type:compound • Quick Search: b1200 • Search -> Genes/Proteins/RNAs • Enzymes using Mg2+ as a cofactor • Search -> Compounds • 300 <= MW <= 320 and containing N

  14. Shared Display Characteristics • Gene-Reaction schematic • Citations and comments • Database Links • Classes

  15. Gene-Reaction Schematic • Drawn in reaction, protein, and gene windows • Representations (ArgB) • Genes are boxes on the right • Proteins are circles in the middle – numbers show complexes • Reactions in box on left, with E.C. number if available • Allows navigation between genes, proteins, rxns • Links proteins with shared reactions • ArgD • Links members of protein complexes • Pol III – extreme example

  16. Citations and Comments • Citations in mnemonic form • Click on citation – go to citations at bottom of page • Click there, go to PubMed ref, if available

  17. Database Links • Unification links (info about the protein elsewhere) • PDB • PIR • RefSeq • UniProt • Relationship links: • PDB-Homolog-P34554

  18. Desktop Mode

  19. Desktop Mode • Linux/PC, Windows/PC, Macintosh

  20. Desktop Window Layout • One Large Window • Several Panes: • Display pane • Command menu • LISP listener

  21. Menus • Main command menu • Single-choice menu • Multiple-choice menu (e.g. after a search) • Aborting out of menus • Click Cancel or No Select • Click outside the menu • Type ^z

  22. Using the Mouse • Left mouse button: to invoke specific commands and for hypertext navigation • Right mouse button: to bring up menus of additional operations (for example, when editing a frame) • Mouse documentation line (shows what you’re over, what you can do)

  23. Queries with Multiple Answers • Results in form of a menu to: • select one • some • all • Answer List • Next Answer

  24. Organism Pages • All Organisms Page – Starting Page • Organism grouping • Summary of organisms • Single organism page • PGDB authors, statistics

  25. Select Current Organism • From All Organisms Page • Through organism selector

  26. Pathway Mode Commands • Search by pathway name • Search by substring • Search by class • Search by substrates (can pick role in pathway)

  27. What’s in a Pathway Frame? • Go to arginine biosynthesis I (from ArgD) • Intermediates and reactions • Can toggle level of detail • Feedback regulation can be shown • Locations of mapped genes • Genetic regulation schematic • Note presence of comments, citations, class hierarchy

  28. Reaction Mode Commands • Search by reaction name • Search by E.C. # • Search by class (another E.C. interface) • Search by pathway • Search by substrates

  29. What’s in a Reaction Frame? • Search by EC for 2.6.1.11 (pick one) • Picture of reaction with clickable compounds • Pathways the reaction is involved in • Place in class hierarchy • Enzymes carrying out reaction (note schematic)

  30. Protein Mode Commands • Search by protein name • Search by substring • Search by pathway • Search by organism (MetaCyc) • Search by UniProt Acc • Search by GO term • Search by MultiFun term • Search by Weight, pI • Search by modulation of activity

  31. What’s in a Protein Frame? • Sample frame (ArgD) • Synonyms, general features, comments • Unification links, gene-reaction schematic • GO terms • Enzymatic reaction frames – how this protein carries out that reaction (bridging the two) • Evidence codes

  32. Gene Mode Commands • Search by gene name (can also put in TU IDs) • Search by substring • Get gene by class • Basically the same for RNAs

  33. What’s in a Gene Page? • Sample frame (argC) • Synonyms, classification (GO), link to browser • Unification links, gene-reaction schematic • Regulation schematic • Gene local context and TUs

  34. What’s in a Transcription Unit Page? • Sample frame (argCBH) • Genes in context, with TFs • Promoter with start site and citations • TF binding sites, with citations • Regulatory interactions (ilvL attenuator in TU524)

  35. Compound Mode Commands • Search compound by name • Search compound by substring • Search by SMILES (structure) • Search by class • Advanced search

  36. The SMILES Language • Simplified Molecular Input Line Entry System • Formal language for describing chemical structures • Used within the Pathway Tools in a substructure search • Case is significant (lowercase for aromatic rings) • Examples: formate C(=O)O malate OC(=O)CC(O)C(O)=O • For more information, see the Help facility

  37. What’s in a Compound Page? • Sample (N-acetylglutamyl-phosphate) • Synonyms, empirical formula, MW, links • Structure • SMILES code • Pathways and reactions involving this compound

  38. Miscellaneous Commands • History commands • Answer-List commands • Clone window command • Fix window and unfix window commands • Other commands: • Print to file (makes a postscript) • Help • Preferences • Exit

  39. History List • Backward history • Forward history • Select from history

  40. User Preferences • Color • Layout • Compound window • Reaction window • Pathway window • History/Answer list • Reverting and saving user preferences

  41. Lab Exercises • Set up personal preferences for: Color Layout (set number of windows to 2) • Save new preferences • Play with settings for Compound, Reaction, Pathway, and Overview windows. • Choose settings for History/Answer List preferences

  42. Lab Exercises • Retrieve compounds containing a formate group • Retrieve compounds adenine and uracil using class query • Retrieve reaction with EC# 5.3.1.9 • Retrieve all reactions in the class sulfurtransferases • Retrieve all reactions involved in proline biosynthesis • Retrieve all reactions where glutamate appears on left side • genes coding for enzymes involved in the degradation of short-chain fatty acids

  43. Lab Exercises • Retrieve all enzymes involved in purine biosynthesis • Retrieve all kinases • Display region spanning from 10 % - 20 % of E. coli chromosome • Display chromosomal region around gene aroA • Display a map showing all chaperone genes

  44. Lab Exercises • Retrieve all chaperone genes • Retrieve gene aroA • Find the glutamine biosynthesis pathway by issuing each of the three types of queries in Pathway mode.

  45. Lab Exercises • Clone window • Navigate in the cloned window • Set preferences so Navigator displays 2 windows • Navigate by clicking on live objects • Fix Window • Navigate in unfixed window • Fix second window and then click on live object

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