ThePathwayGenomeNavigator

1、The Pathway/Genome Navigator(These slides are a guide as you experiment with the Navigator)Pathway/Genome Navigator topicsGetting started with the NavigatorOrganism pagesQueries in generalObject displays and queriesMiscellaneous commandsUser preferencesLab exercisesIntroductionNavigator runs both on

2、 the desktop and on the webThe desktop version generally has more capabilitiesDesktop LayoutOne Large WindowSeveral Panes:Display paneCommand menuLISP listenerMenusMain command menuSingle-choice menuMultiple-choice menu (e.g. after a search)Aborting out of menusClick Cancel or No SelectClick outside

3、 the menuType zUsing the MouseLeft mouse button: to invoke specific commands and for hypertext navigationRight mouse button: to bring up menus of additional operations (for example, when editing a frame)Middle mouse button: for very specialized uses (you probably wont use it)Mouse documentation line

4、 (shows what youre over, what you can do)Organism PagesAll Organisms PageOrganism groupingSummary of organismsSingle organism pageSummary of organism statsNotion of current organismCommand mode queriesComparative analysesClicking through links organism continuityQuery Facilities topicsDirect queries

5、Queries with multiple answersIndirect approach: navigationHistory ListComplex queriesDirect QueriesDone by type (for example, search for proteins)Searches common to all typesBy name/frame ID must be exact (though there are synonyms)By substring if you dont know an exact nameParticular searches by ty

6、peWill be handled as we cover each typeQueries with multiple answersResults in form of a menu to:select onesomeallAnswer ListNext AnswerIndirect QueriesRelated objectsObjects are clickableObjects are color-coded by typeHistory ListBackward historyForward historySelect from historyComplex QueriesWrit

7、e queries in LISPMust understand features of schemaclass namesslot namesPathway tools site has example searchesDefinitely learnableCan place results on the answer listObject Displays and Queries topicsShared display characteristicsSearching within each category of objectWhats in each kind of object

8、frame?Looking at genomes and orthologsShared Display CharacteristicsGene-Reaction schematicCitations and commentsDatabase LinksClassesGene-Reaction SchematicDrawn in reaction, protein, and gene windowsRepresentations (ArgB)Genes are boxes on the rightProteins are circles in the middle numbers show c

9、omplexesReactions in box on left, with E.C. number if availableAllows navigation between genes, proteins, rxnsLinks proteins with shared reactionsArgDLinks members of protein complexesPol III extreme exampleCitations and CommentsCitations in mnemonic formClick on citation go to citations at bottom o

10、f pageClick there, go to PubMed ref, if availableDatabase LinksUnification links (info about the protein elsewhere)PDBPIRRefSeqUniProtGene page: For coli, we added links to coli-specific sitesRelationship links:PDB-Homolog-P34554Class HierarchiesReactionsEnzyme-nomenclature system (full EC system in

11、 MetaCyc only)ProteinsGene Ontology terms are assigned to proteinsCan also assign MultiFun termsCompoundsPathwaysMenu CategoriesPathwayReactionProtein(RNA)GeneCompoundPathway Mode CommandsSearch by pathway nameSearch by substringSearch by classSearch by substrates (can pick role in pathway)Whats in

12、a pathway frame?Go to arginine biosynthesis I (from ArgD)Intermediates and reactionsCan toggle level of detailFeedback regulation can be shownLocations of mapped genesGenetic regulation schematicNote presence of comments, citations, class hierarchyReaction Mode CommandsSearch by reaction nameSearch

13、by E.C. #Search by class (another E.C. interface)Search by pathwaySearch by substratesWhats in a reaction frame?Search by EC for 2.6.1.11 (pick one)Picture of reaction with clickable compoundsPathways the reaction is involved inPlace in class hierarchyEnzymes carrying out reaction (note schematic)Pr

14、otein Mode CommandsSearch by protein nameSearch by substringSearch by pathwaySearch by organism (MetaCyc)Search by UniProt AccSearch by GO termSearch by MultiFun termSearch by Weight, pISearch by modulation of activityWhats in a protein frame?Sample frame (ArgD)Synonyms, general features, commentsUn

15、ification links, gene-reaction schematicGO termsEnzymatic reaction frames how this protein carries out that reaction (bridging the two)Evidence codesGene Mode CommandsSearch by gene name (can also put in TU IDs)Search by substringGet gene by classBasically the same for RNAsWhats in a gene frame?Samp

16、le frame (argC)Synonyms, classification (GO), link to browserUnification links, gene-reaction schematicRegulation schematicGene local context and TUsWhats in a TU frame?Sample frame (argCBH)Genes in context, with TFsPromoter with start site and citationsTF binding sites, with citationsRegulatory int

17、eractions (ilvL attenuator in TU524)Compound Mode CommandsSearch compound by nameSearch compound by substringSearch by SMILES (structure)Search by classAdvanced searchThe SMILES LanguageSimplified Molecular Input Line Entry SystemFormal language for describing chemical structuresUsed within the Path

18、way Tools in a substructure searchCase is significant (lowercase for aromatic rings)Examples:formate C(=O)Omalate OC(=O)CC(O)C(O)=OFor more information, see the Help facilityWhats in a compound frame?Sample (N-acetylglutamyl-phosphate)Synonyms, empirical formula, MW, linksStructure (you can add thes

19、e in editors)SMILES codePathways and reactions involving this compoundMiscellaneous CommandsHistory commandsAnswer-List commandsClone window commandFix window and unfix window commandsOther commands:Print to file (makes a postscript)HelpPreferencesExitUser PreferencesColorLayoutCompound windowReacti

20、on windowPathway windowHistory/Answer listReverting and saving user preferencesLab ExercisesSet up personal preferences for:ColorLayout (set number of windows to 2)Save new preferencesPlay with settings for Compound, Reaction, Pathway, and Overview windows.Choose settings for History/Answer List pre

21、ferencesLab ExercisesRetrieve compounds containing a formate groupRetrieve compounds adenine and uracil using class query Retrieve reaction with EC# 5.3.1.9Retrieve all reactions in the class sulfurtransferasesRetrieve all reactions involved in proline biosynthesisRetrieve all reactions where glutamate appears on