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The Pathway/Genome Navigator

The Pathway/Genome Navigator. Overview. Data page types General query strategies Web queries Desktop Pathway Tools User preferences Lab exercises. Pathway/Genome Navigator. Navigator runs both on the desktop and on the web Desktop version Runs faster More capabilities

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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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