1. SRI International Bioinformatics 1 Overview of the Pathway/Genome Navigator (These slides are a guide as you experiment with the Navigator)

2. SRI International Bioinformatics 2 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 3 Introduction Navigator runs both on the desktop and on the web The two versions are similar, but each has unique features

4. SRI International Bioinformatics 4 Desktop Mode -- Introduction

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

6. SRI International Bioinformatics 6 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 7 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) Middle mouse button: for specialized uses (you probably won’t use it) Pop-ups (shows information on what you’re over)

8. SRI International Bioinformatics 8 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 9 Query Facilities – topics Direct queries l Queries with multiple answers Indirect approach: navigation History List Complex queries

10. SRI International Bioinformatics 10 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 Quick Search

11. SRI International Bioinformatics 11 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 12 Indirect Queries Related objects Objects are clickable Objects are color-coded by type

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

14. SRI International Bioinformatics 14 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. SRI International Bioinformatics 15 Overview of Object Displays

16. SRI International Bioinformatics 16 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

17. SRI International Bioinformatics 17 Shared Display Characteristics Gene-Reaction schematic Citations and comments Database Links Classes

18. SRI International Bioinformatics 18 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

19. SRI International Bioinformatics 19 Citations and Summaries Citations in mnemonic form Click on citation – go to citations at bottom of page Click there, go to PubMed ref, if available

20. SRI International Bioinformatics 20 Database Links Unification links (info about the gene/protein/RNA elsewhere) l PIR l RefSeq l UniProt l Gene page: E.g. for E. coli, we added links to E. coli -specific sites Relationship links: l PDB

21. SRI International Bioinformatics 21 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

22. SRI International Bioinformatics 22 Menu Categories Pathway Reaction Protein RNA Gene Compound

23. SRI International Bioinformatics 23 Pathway Mode Commands Search by pathway name Search by substring Search by class Search by substrates (can pick role in pathway)

24. SRI International Bioinformatics 24 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 summaries, citations, class hierarchy

25. SRI International Bioinformatics 25 Reaction Mode Commands Search by reaction name Search by E.C. # Search by class (another E.C. interface) Search by pathway Search by substrates

26. SRI International Bioinformatics 26 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)

27. SRI International Bioinformatics 27 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

28. SRI International Bioinformatics 28 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

29. SRI International Bioinformatics 29 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

30. SRI International Bioinformatics 30 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

31. SRI International Bioinformatics 31 What’s in a TU frame? Sample frame (argCBH) Genes in context, with TFs Promoter with transcription start site and citations TF binding sites, with citations Regulatory interactions (ilvL attenuator in TU524)

32. SRI International Bioinformatics 32 Compound Mode Commands Search compound by name Search compound by substring Search by SMILES (structure) Search by class Advanced search

33. SRI International Bioinformatics 33 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

34. SRI International Bioinformatics 34 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

35. SRI International Bioinformatics 35 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

36. SRI International Bioinformatics 36 User Preferences Color Layout Compound window Reaction window Pathway window History/Answer list Reverting and saving user preferences

37. SRI International Bioinformatics 37 Lab Exercises – Desktop Version

38. SRI International Bioinformatics 38 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

39. SRI International Bioinformatics 39 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

40. SRI International Bioinformatics 40 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

41. SRI International Bioinformatics 41 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.

42. SRI International Bioinformatics 42 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

43. SRI International Bioinformatics 43 The Web Interface: BioCyc Ron Caspi

44. SRI International Bioinformatics 44 Help is One Click Away!

45. SRI International Bioinformatics 45 The Web Account System

46. SRI International Bioinformatics 46 The Web Account System Creating a web account enables you to: Save Object Groups Define page formatting preferences Define Overview layout preferences Save organism groups for comparative analysis

47. SRI International Bioinformatics 47 Save Organism Groups with Web Accounts Note the My Lists tab on the multi-organism selector for comparative analyses. When you perform comparative analyses, you can easily save groups of organisms for re-using at a later time.

48. SRI International Bioinformatics 48 Define a Favorite Database with Web Accounts If you create a web account, you can define a favorite database that will be opened by default when you login

49. SRI International Bioinformatics 49 Searching the Database

50. SRI International Bioinformatics 50 Why the Need for Dedicated Search Tools Search BioCyc for “L-arginine” 2080 results Need to have specific tools for finding exactly what we search for.

51. SRI International Bioinformatics 51 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

52. SRI International Bioinformatics 52 Selecting the Database You can only search one database at a time*! * With the exception of Google searches 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 l Select by Taxonomy All subsequent searches will apply to that database

53. SRI International Bioinformatics 53 Two organism/database selectors! There are two different organism selectors in BioCyc The first one is the selector found at the top of the page, which selects a single organism/database, which is then used for most searches. The second one is a multi-organism selector, used for comparative analyses (See Tools → Comparative analysis → Choose organisms).

54. SRI International Bioinformatics 54 The Quick Search Box What can you type here: l Gene names (dnaA ) l Compound name (L-lysine) l Pathway name (peptidoglycan biosynthesis) l Reaction name (lysine decarboxylase) l Protein name (peptidase) l EC number (1.3.1.26) l Organism name (Escherichia coli) l Frame ID (CPLX-8024) l GO term (0006086) l Links to other databases (O33998) l An exact term using the format (Peptidase D search:exact) l Limited term (hydrogen type:compound) What doesn’t work: l Exact text using the Google format (“peptidase D”)

55. SRI International Bioinformatics 55 Quick Search Results Results are divided into multiple categories

56. SRI International Bioinformatics 56 Examples of searches performed by users of the BioCyc website: SuccessfulUnsuccessful Ascorbate pheV EC 3.4.17.5Transmembrane helix 6 Sigma factor3.4.24.B11 Polysulfide reductaseABC cobalt transporter Entner-Doudoroff pathwayaffinity of DnaA Cyanobacteria DnaA A simple auto-correction mechanism tries to correct typos. For example, searching for “sacrosine” will find “sarcosine”.

57. SRI International Bioinformatics 57 Quick Gene Search Useful when only interested in genes. For example, compare the results when searching for “dnaA” by using the Quick Search and Gene Search buttons.

58. SRI International Bioinformatics 58 The Search Menu 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)

59. SRI International Bioinformatics 59 Google This Site The BioCyc site is indexed by Google You can launch a Google text search from: 1. Search → Google This Site 2. The alternative searches box that appears on Quick Search results pages

60. SRI International Bioinformatics 60 Object-Specific Searches The first four items in the search menu provide a medium-level search interface against single types of objects Use of filtering 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

61. SRI International Bioinformatics 61 Compound Search List All buttons – quick way to get complete lists Examples for compound searching:

62. SRI International Bioinformatics 62 Search Genes/Proteins/RNAs List All buttons – quick way to get complete lists Extensive filtering options

63. SRI International Bioinformatics 63 Search Pathways

64. SRI International Bioinformatics 64 Advanced Search The BioVelo query language SAQP: Structured Advanced Query Page l Permits the definition of complex searches without mastering BioVelo. To learn more about the advanced query interface, see online documentation.

65. SRI International Bioinformatics 65 Sequence Search by BLAST Nothing unusual here – a regular BLAST interface that permits BLASTing sequences against BioCyc PGDBs. The results are linked to the PGDB gene/protein pages

66. SRI International Bioinformatics 66 The desktop version of Pathway Tools allows definition of growth media, gene knockout growth information, and growth data for phenotype microarray plates. Growth Media and Phenotype

67. SRI International Bioinformatics 67 EcoCyc-Specific Searches: Growth Media Search for growth media based on: name compounds present compounds not present observed growth

68. SRI International Bioinformatics 68 EcoCyc-Specific Searches: Textpresso Mining E. coli literature poses special challenges – because almost every molecular biology paper references E. coli The solution – EcoCyc Textpresso! An E. coli only collection of literature 30,000 full-text articles and 6,500 abstracts. Full text literature searches Results presented at bottom of page

69. SRI International Bioinformatics 69 Web Version Lab Exercises

70. SRI International Bioinformatics 70 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

71. SRI International Bioinformatics 71 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