1. The Pathway/Genome Navigator (These slides are a guide as you experiment with the Navigator)

2. SRI International Bioinformatics Pathway/Genome Navigator – topics Getting started with the Navigator Organism pages Queries in general Object displays and queries Miscellaneous commands User preferences Lab exercises

3. SRI International Bioinformatics Introduction Navigator runs both on the desktop and on the web The desktop version generally has more capabilities, but each has unique features

4. Desktop Mode -- Introduction

5. SRI International Bioinformatics Desktop Layout One Large Window Several Panes: l Display pane l Command menu l LISP listener

6. SRI International Bioinformatics Desktop Menus Main command menu Single-choice menu Multiple-choice menu (e.g. after a search) Aborting out of menus l Click Cancel or No Select l Click outside the menu l Type ^z

7. SRI International Bioinformatics 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) Middle mouse button: for very specialized uses (you probably won’t use it) Mouse documentation line (shows what you’re over, what you can do)

8. SRI International Bioinformatics Organism Pages All Organisms Page l Organism grouping l Summary of organisms Single organism page l Summary of organism stats Notion of current organism l Command mode queries l Comparative analyses l Clicking through links – organism continuity

9. SRI International Bioinformatics Query Facilities – topics Direct queries l Queries with multiple answers Indirect approach: navigation History List Complex queries

10. SRI International Bioinformatics Direct Queries Done by type (for example, search for proteins) Searches common to all types l By name/frame ID – must be exact (though there are synonyms) l By substring – if you don’t know an exact name Particular searches by type l Will be handled as we cover each type

11. SRI International Bioinformatics Queries with multiple answers Results in form of a menu to: l select one l some l all Answer List l Next Answer

12. SRI International Bioinformatics Indirect Queries Related objects Objects are clickable Objects are color-coded by type

13. SRI International Bioinformatics History List Backward history Forward history Select from history

14. SRI International Bioinformatics Writing Complex Queries Web Search  Advanced Write queries in LISP l Must understand features of schema u class names u slot names l Pathway tools site has example searches l Definitely learnable l Can place results on the answer list

15. Using the BioCyc Web Site and Other Pathway Tools Based Web Sites

16. SRI International Bioinformatics BioCyc Searches Multiple searches available for finding information in different ways The easiest searches to use are fairly coarse Start by selecting database to search Simplest search: Quick Search l At upper right of most pages Search Menu l Object-specific searches l Advanced search l Ontologies search l Google search l BLAST search l Search of full-text articles (EcoCyc only)

17. SRI International Bioinformatics Database Selector Click on word “change” under Search menu or under Quick Search button In resulting selector, choose a PGDB l Start typing a word in organism name l Click on letter to navigate to organisms starting with that letter l Click a frequently used PGDB All subsequent searches will apply to that database

18. SRI International Bioinformatics Quick Search Enter a search string in quick search box Gene Search button searches gene names and synonyms Quick Search button searches names and synonyms of l Genes l Proteins l RNAs l GO terms l Compounds l Reactions l Pathways l Transcription Units Result page shows all matching objects, organized by object type

19. SRI International Bioinformatics Object Specific Searches Allow you to create detailed searches against single types of objects Specify multiple constraints on the object you want to find Click on triangles at the left to expand or hide filters Note that if a filter is hidden it will not be used in a search

20. SRI International Bioinformatics BioCyc Web Site: Object Page Types Genes + Gene Products l Enzymes, transporters, transcription factors, others l Extensive comments and citations l Monomers and multimers are represented, and in different chemical states Reactions Pathways Compounds Searches are organized around these page types

21. SRI International Bioinformatics Textpresso Search EcoCyc only Searches full text of a large corpus of articles (2010: 24,000 articles) Keyword and/or ontology-based searches Scope is sentence by default Results presented at bottom of page

22. SRI International Bioinformatics Textpresso Search Keyword search examples: l tryptophan yanofsky -- keyword and l tryptophan,yanofsky -- keyword or l attenuation –tryptophan – exclude tryptophan l “excess tryptophan” -- phrase Ontology search examples:

23. SRI International Bioinformatics Additional Searches Advanced search allows user to formulate detailed multi-object searches Ontology searches allow the user to drill down through a classification system to find information of interest Google search performs search across all web pages within this site for words of interest BLAST search performs sequence search against a single specified genome

24. SRI International Bioinformatics Web Account System Page formatting preferences Omics viewer preferences Comparative analysis preferences Receive email updates on new releases

25. Overview of Object Displays

26. SRI International Bioinformatics Object Displays and Queries Shared display characteristics Searching within each category of object What’s in each kind of object frame? Looking at genomes and orthologs

27. SRI International Bioinformatics Shared Display Characteristics Gene-Reaction schematic Citations and comments Database Links Classes

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

29. SRI International Bioinformatics 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

30. SRI International Bioinformatics Database Links Unification links (info about the protein elsewhere) l PDB l PIR l RefSeq l UniProt l Gene page: For coli, we added links to coli-specific sites Relationship links: l PDB-Homolog-P34554

31. SRI International Bioinformatics Class Hierarchies Reactions l Enzyme-nomenclature system (full EC system in MetaCyc only) Proteins l Gene Ontology terms are assigned to proteins l Can also assign MultiFun terms Compounds Pathways

32. SRI International Bioinformatics Menu Categories Pathway Reaction Protein (RNA) Gene Compound

33. SRI International Bioinformatics Pathway Mode Commands Search by pathway name Search by substring Search by class Search by substrates (can pick role in pathway)

34. SRI International Bioinformatics 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

35. SRI International Bioinformatics Reaction Mode Commands Search by reaction name Search by E.C. # Search by class (another E.C. interface) Search by pathway Search by substrates

36. SRI International Bioinformatics 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)

37. SRI International Bioinformatics 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

38. SRI International Bioinformatics 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

39. SRI International Bioinformatics 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

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

41. SRI International Bioinformatics What’s in a TU frame? 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)

42. SRI International Bioinformatics Compound Mode Commands Search compound by name Search compound by substring Search by SMILES (structure) Search by class Advanced search

43. SRI International Bioinformatics 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

44. SRI International Bioinformatics What’s in a compound frame? Sample (N-acetylglutamyl-phosphate) Synonyms, empirical formula, MW, links Structure (you can add these in editors) SMILES code Pathways and reactions involving this compound

45. SRI International Bioinformatics Miscellaneous Commands History commands Answer-List commands Clone window command Fix window and unfix window commands Other commands: l Print to file (makes a postscript) l Help l Preferences l Exit

46. SRI International Bioinformatics User Preferences Color Layout Compound window Reaction window Pathway window History/Answer list Reverting and saving user preferences

47. Lab Exercises – Desktop Version

48. SRI International Bioinformatics 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

49. SRI International Bioinformatics Desktop 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

50. SRI International Bioinformatics Desktop 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

51. SRI International Bioinformatics Desktop 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.

52. SRI International Bioinformatics Desktop 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

53. Web Version Lab Exercises

54. SRI International Bioinformatics Web Lab Exercises In EcoCyc: Retrieve gene aroA Retrieve all kinases Retrieve all chaperone genes using two different approaches Retrieve all membrane proteins that cite an article by Gross Retrieve all genes whose product interacts with ppGpp as a regulator or cofactor

55. SRI International Bioinformatics Web Lab Exercises In MetaCyc: Retrieve reaction with EC# 5.3.1.9 Retrieve compounds adenine and uracil using ontology search Retrieve all reactions involving glutamate as a substrate Find genes coding for enzymes involved in the degradation of short-chain fatty acids Find all pathways involved in degradation of arginine