The Pathway/Genome Navigator

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The Pathway/Genome Navigator
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Overview

• Data page types
• General query strategies
• Web queries
• Desktop Pathway Tools
• User preferences
• Lab exercises

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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

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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
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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 dont know an exact name
• Searches that are specific to object type

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Indirect Queries

• Find an object by searching for an object that is
  probably related to it
• Then navigate to the object you seek

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Complex Queries

• Define multi-criteria searches
• System returns all objects that meet those
  criteria

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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

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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

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Select Current Organism

• Click on change
• Under Quick Search button
• Bottom of Search menu
• Bottom of Tools menu
• Select by typing or clicking

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Organism Pages

• Tools -gt Reports -gt Summary statistics
• PGDB authors, statistics

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Sample Web Searches for EcoCyc

• Quick Search xyl
• Quick Search trpa typegene
• Quick Search b1200
• Search -gt Genes/Proteins/RNAs
• 40 lt MW lt 50 and 5.5 lt pI lt 6.0
• 3000000 lt Map-Position lt 3500000 and
• Has Gene Ontology term locomotion
• (under Biological Process)

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Sample Web Searches for HumanCyc

• Quick Search dopamine
• Quick Search dopamine typecompound
• Quick Search b1200
• Search -gt Genes/Proteins/RNAs
• Enzymes using Mg2 as a cofactor
• Search -gt Compounds
• 300 lt MW lt 320 and containing N

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Shared Display Characteristics

• Gene-Reaction schematic
• Citations and comments
• Database Links
• Classes

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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

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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

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Database Links

• Unification links (info about the protein
  elsewhere)
• PDB
• PIR
• RefSeq
• UniProt
• Relationship links
• PDB-Homolog-P34554

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Class Hierarchies

• Reactions
• Enzyme-nomenclature system (full EC system in
  MetaCyc only)
• Proteins
• Gene Ontology terms are assigned to proteins
• Can also assign MultiFun terms
• Compounds
• Pathways

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Desktop Mode
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Desktop Mode

• Linux/PC, Windows/PC, Macintosh

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Desktop Window Layout

• One Large Window
• Several Panes
• Display pane
• Command menu
• LISP listener

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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

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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 youre over,
  what you can do)

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Queries with Multiple Answers

• Results in form of a menu to
• select one
• some
• all
• Answer List
• Next Answer

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Organism Pages

• All Organisms Page Starting Page
• Organism grouping
• Summary of organisms
• Single organism page
• PGDB authors, statistics

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Select Current Organism

• From All Organisms Page
• Through organism selector

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Pathway Mode Commands

• Search by pathway name
• Search by substring
• Search by class
• Search by substrates (can pick role in pathway)

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Whats 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

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Reaction Mode Commands

• Search by reaction name
• Search by E.C.
• Search by class (another E.C. interface)
• Search by pathway
• Search by substrates

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Whats 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)

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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

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Whats 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

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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

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Whats 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

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Whats 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)

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Compound Mode Commands

• Search compound by name
• Search compound by substring
• Search by SMILES (structure)
• Search by class
• Advanced search

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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

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Whats in a Compound Page?

• Sample (N-acetylglutamyl-phosphate)
• Synonyms, empirical formula, MW, links
• Structure
• SMILES code
• Pathways and reactions involving this compound

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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

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History List

• Backward history
• Forward history
• Select from history

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User Preferences

• Color
• Layout
• Compound window
• Reaction window
• Pathway window
• History/Answer list
• Reverting and saving user preferences

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Program-Based Queries

• Write 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

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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

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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

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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

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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.

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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