The Pathway/Genome Navigator
(These slides are a guide as you
experiment with the Navigator)
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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
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runs both on the desktop and on the
web
 The
desktop version generally has more
capabilities
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Desktop Layout
 One
Large Window
 Several
Panes:
 Display pane
 Command menu
 LISP listener
Menus
 Main
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command menu
 Single-choice
menu
 Multiple-choice
 Aborting
menu (e.g. after a search)
out of menus
 Click Cancel or No Select
 Click outside the menu
 Type ^z
Using the Mouse
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 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)
Organism Pages
 All
Organisms Page
 Organism grouping
 Summary of organisms
 Single
organism page
 Summary of organism stats
 Notion
of current organism
 Command mode queries
 Comparative analyses
 Clicking through links – organism continuity
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Queries with multiple answers
 Results
in form of a menu to:
 select one
 some
 all
 Answer
List
 Next Answer
Indirect Queries
 Related
objects
 Objects
are clickable
 Objects
are color-coded by type
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History List
 Backward
 Forward
 Select
history
history
from history
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Complex Queries
 WWW
Form
 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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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
 Click
in mnemonic form
on citation – go to citations at bottom of
page
 Click
there, go to PubMed ref, if available
Database Links
 Unification
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links (info about the protein
elsewhere)
 PDB
 PIR
 RefSeq
 UniProt
 Gene page: For coli, we added links to coli-specific sites
 Relationship
links:
 PDB-Homolog-P34554
Class Hierarchies
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 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
Menu Categories
 Pathway
 Reaction
 Protein
 (RNA)
 Gene
 Compound
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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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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
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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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What’s in a reaction frame?
 Search
by EC for 2.6.1.11 (pick one)
 Picture
of reaction with clickable compounds
 Pathways
 Place
the reaction is involved in
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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What’s in a protein frame?
 Sample
frame (ArgD)
 Synonyms,
general features, comments
 Unification
links, gene-reaction schematic
 GO
terms
reaction frames – how this protein
carries out that reaction (bridging the two)
 Enzymatic
 Evidence
codes
Gene Mode Commands
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 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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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
What’s in a TU frame?
 Sample
 Genes
frame (argCBH)
in context, with TFs
 Promoter
 TF
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with start site and citations
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
The SMILES Language
 Simplified
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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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What’s in a compound frame?
 Sample
(N-acetylglutamyl-phosphate)
 Synonyms,
 Structure
 SMILES
empirical formula, MW, links
(you can add these in editors)
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
User Preferences
 Color
 Layout
 Compound
window
 Reaction window
 Pathway window
 History/Answer list
 Reverting and saving user preferences
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Lab Exercises
 Set
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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
Lab Exercises
 Retrieve
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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
Lab Exercises
 Retrieve
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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
Lab Exercises
 Retrieve
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all chaperone genes
 Retrieve gene aroA
 Find the glutamine biosynthesis pathway by
issuing each of the three types of queries in
Pathway mode.
Lab Exercises
 Clone
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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