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The Pathway/Genome Navigator
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Bioinformatics
Overview
Data
page types
General
Web
queries
Desktop
User
Lab
query strategies
Pathway Tools
preferences
exercises
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Pathway/Genome Navigator
Navigator
runs both on the desktop and on the
web
Desktop
version
Runs faster
More capabilities
Both
PGDB creation, editing
Reachability analysis, metabolite tracing, object groups
More omics analysis
have capabilities the other does not have
http://biocyc.org/desktop-vs-web-mode.shtml
Data Page Types for
Individual PGDB Objects
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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
Direct Queries
Search
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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 don’t know an exact name
Searches
that are specific to object type
Indirect Queries
Find
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an object by searching for an object that is
probably related to it
Then
navigate to the object you seek
Complex Queries
Define
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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
Create
not recommended
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
Web Searches
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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
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
-> Reports -> Summary statistics
PGDB authors, statistics
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Sample Web Searches for EcoCyc
Quick
Search: xyl
Quick Search: trpa type:gene
Quick Search: b1200
Search
-> Genes/Proteins/RNAs
40 < MW < 50 and 5.5 < pI < 6.0
3000000 < Map-Position < 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 type:compound
Quick Search: b1200
Search
-> Genes/Proteins/RNAs
Enzymes using Mg2+ as a cofactor
Search
-> Compounds
300 <= MW <= 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
Click
in mnemonic form
on citation – go to citations at bottom of
page
Click
there, go to PubMed ref, if available
Database Links
Unification
links (info about the protein
elsewhere)
PDB
PIR
RefSeq
UniProt
Relationship
links:
PDB-Homolog-P34554
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Desktop Mode
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
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)
Mouse
documentation line (shows what you’re
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
Organism Pages
Organisms Page – Starting Page
Organism grouping
Summary of organisms
All
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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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 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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What’s in a Transcription Unit Page?
Sample
Genes
frame (argCBH)
in context, with TFs
Promoter
TF
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 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
History List
Backward
Forward
Select
history
history
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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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