1、The Pathway/Genome Navigator,(These slides are a guide as you experiment with the Navigator),Pathway/Genome Navigator topics,Getting started with the Navigator Organism pages Queries in general Object displays and queries Miscellaneous commands User preferences Lab exercises,Introduction,Navigator r
2、uns both on the desktop and on the webThe desktop version generally has more capabilities,Desktop Layout,One Large WindowSeveral Panes: Display pane Command menu LISP listener,Menus,Main command menuSingle-choice menuMultiple-choice menu (e.g. after a search)Aborting out of menus Click Cancel or No
3、Select Click outside the menu Type z,Using the Mouse,Left 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)M
4、ouse documentation line (shows what youre over, what you can do),Organism Pages,All Organisms Page Organism grouping Summary of organismsSingle organism page Summary of organism statsNotion of current organism Command mode queries Comparative analyses Clicking through links organism continuity,Query
5、 Facilities topics,Direct queries Queries with multiple answersIndirect approach: navigationHistory ListComplex queries,Direct Queries,Done by type (for example, search for proteins) Searches common to all types By name/frame ID must be exact (though there are synonyms) By substring if you dont know
6、 an exact name Particular searches by type Will be handled as we cover each type,Queries with multiple answers,Results in form of a menu to: select one some allAnswer List Next Answer,Indirect Queries,Related objectsObjects are clickableObjects are color-coded by type,History List,Backward historyFo
7、rward historySelect from history,Complex Queries,WWW FormWrite queries in LISP Must understand features of schema class names slot names Pathway tools site has example searches Definitely learnable Can place results on the answer list,Object Displays and Queries topics,Shared display characteristics
8、Searching within each category of objectWhats in each kind of object frame?Looking at genomes and orthologs,Shared Display Characteristics,Gene-Reaction schematicCitations and commentsDatabase LinksClasses,Gene-Reaction Schematic,Drawn in reaction, protein, and gene windowsRepresentations (ArgB) Gen
9、es 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,Citations a
10、nd Comments,Citations in mnemonic formClick on citation go to citations at bottom of pageClick there, go to PubMed ref, if available,Database Links,Unification links (info about the protein elsewhere) PDB PIR RefSeq UniProt Gene page: For coli, we added links to coli-specific sitesRelationship links
11、: PDB-Homolog-P34554,Class Hierarchies,Reactions Enzyme-nomenclature system (full EC system in MetaCyc only)Proteins Gene Ontology terms are assigned to proteins Can also assign MultiFun termsCompoundsPathways,Menu Categories,Pathway Reaction Protein (RNA) Gene Compound,Pathway Mode Commands,Search
12、by pathway nameSearch by substringSearch by classSearch by substrates (can pick role in pathway),Whats in 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 schemat
13、icNote presence of comments, citations, class hierarchy,Reaction Mode Commands,Search by reaction nameSearch by E.C. #Search by class (another E.C. interface)Search by pathwaySearch by substrates,Whats in a reaction frame?,Search by EC for 2.6.1.11 (pick one)Picture of reaction with clickable compou
14、ndsPathways the reaction is involved inPlace in class hierarchyEnzymes carrying out reaction (note schematic),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 Weig
15、ht, pI Search by modulation of activity,Whats in a protein frame?,Sample frame (ArgD)Synonyms, general features, commentsUnification links, gene-reaction schematicGO termsEnzymatic reaction frames how this protein carries out that reaction (bridging the two)Evidence codes,Gene Mode Commands,Search b
16、y gene name (can also put in TU IDs)Search by substringGet gene by classBasically the same for RNAs,Whats in a gene frame?,Sample frame (argC)Synonyms, classification (GO), link to browserUnification links, gene-reaction schematicRegulation schematicGene local context and TUs,Whats in a TU frame?,Sa
17、mple frame (argCBH)Genes in context, with TFsPromoter with start site and citationsTF binding sites, with citationsRegulatory interactions (ilvL attenuator in TU524),Compound Mode Commands,Search compound by nameSearch compound by substringSearch by SMILES (structure)Search by classAdvanced search,T
18、he 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
19、 Help facility,Whats in a compound frame?,Sample (N-acetylglutamyl-phosphate)Synonyms, empirical formula, MW, linksStructure (you can add these in editors)SMILES codePathways and reactions involving this compound,Miscellaneous Commands,History commands Answer-List commands Clone window command Fix w
20、indow and unfix window commands Other commands: Print to file (makes a postscript) Help Preferences Exit,User Preferences,Color Layout Compound window Reaction window Pathway window History/Answer list Reverting and saving user preferences,Lab Exercises,Set up personal preferences for:ColorLayout (s
21、et 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,Lab Exercises,Retrieve compounds containing a formate group Retrieve compounds adenine and uracil using class query Retrieve r
22、eaction 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,Lab Exercises,Retrieve a
23、ll enzymes involved in purine biosynthesis Retrieve all kinases Display region spanning from 10 % - 20 % of E. coli chromosomeDisplay chromosomal region around gene aroA Display a map showing all chaperone genes,Lab Exercises,Retrieve all chaperone genes Retrieve gene aroA Find the glutamine biosynt
24、hesis pathway by issuing each of the three types of queries in Pathway mode.,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,
