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SRI InternationalBioinformatics
Overview
Data page types
General query strategies
Web queries
Desktop Pathway Tools
User preferences
Lab exercises
SRI InternationalBioinformaticsPathway/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
SRI InternationalBioinformaticsData 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
SRI InternationalBioinformaticsDirect 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 don’t know an exact name
Searches that are specific to object type
SRI InternationalBioinformaticsIndirect Queries
Find an object by searching for an object that is probably related to it
Then navigate to the object you seek
SRI InternationalBioinformaticsComplex Queries
Define multi-criteria searches
System returns all objects that meet those criteria
SRI InternationalBioinformaticsBioCyc 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
SRI InternationalBioinformaticsWeb 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
SRI InternationalBioinformaticsSelect Current Organism
Click on “change” Under Quick Search button Bottom of Search menu Bottom of Tools menu
Select by typing or clicking
SRI InternationalBioinformaticsOrganism Pages
Tools -> Reports -> Summary statistics PGDB authors, statistics
SRI InternationalBioinformaticsSample Web Searches for
EcoCyc
Quick Search: xylQuick Search: trpa type:geneQuick 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)
SRI InternationalBioinformaticsSample Web Searches for
HumanCyc
Quick Search: dopamineQuick Search: dopamine type:compoundQuick Search: b1200
Search -> Genes/Proteins/RNAs Enzymes using Mg2+ as a cofactor
Search -> Compounds 300 <= MW <= 320 and containing N
SRI InternationalBioinformaticsShared Display Characteristics
Gene-Reaction schematic
Citations and comments
Database Links
Classes
SRI InternationalBioinformaticsGene-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, rxnsLinks proteins with shared reactions
ArgDLinks members of protein complexes
Pol III – extreme example
SRI InternationalBioinformaticsCitations and Comments
Citations in mnemonic form
Click on citation – go to citations at bottom of page
Click there, go to PubMed ref, if available
SRI InternationalBioinformaticsDatabase Links
Unification links (info about the protein elsewhere)
PDB PIR RefSeq UniProt
Relationship links: PDB-Homolog-P34554
SRI InternationalBioinformatics
Desktop Window Layout
One Large Window
Several Panes: Display pane Command menu LISP listener
SRI InternationalBioinformaticsMenus
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
SRI InternationalBioinformaticsUsing 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 you’re over, what you can do)
SRI InternationalBioinformaticsQueries with Multiple Answers
Results in form of a menu to: select one some all
Answer List Next Answer
SRI InternationalBioinformaticsOrganism Pages
All Organisms Page – Starting Page Organism grouping Summary of organisms
Single organism page PGDB authors, statistics
SRI InternationalBioinformaticsSelect Current Organism
From All Organisms Page
Through organism selector
SRI InternationalBioinformaticsPathway Mode Commands
Search by pathway name
Search by substring
Search by class
Search by substrates (can pick role in pathway)
SRI InternationalBioinformaticsWhat’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
SRI InternationalBioinformaticsReaction Mode Commands
Search by reaction name
Search by E.C. #
Search by class (another E.C. interface)
Search by pathway
Search by substrates
SRI InternationalBioinformaticsWhat’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)
SRI InternationalBioinformaticsProtein Mode Commands
Search by protein nameSearch by substringSearch by pathwaySearch by organism (MetaCyc)Search by UniProt AccSearch by GO termSearch by MultiFun termSearch by Weight, pISearch by modulation of activity
SRI InternationalBioinformaticsWhat’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
SRI InternationalBioinformaticsGene Mode Commands
Search by gene name (can also put in TU IDs)
Search by substring
Get gene by class
Basically the same for RNAs
SRI InternationalBioinformaticsWhat’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
SRI InternationalBioinformaticsWhat’s 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)
SRI InternationalBioinformaticsCompound Mode Commands
Search compound by name
Search compound by substring
Search by SMILES (structure)
Search by class
Advanced search
SRI InternationalBioinformaticsThe SMILES Language
Simplified Molecular Input Line Entry SystemFormal language for describing chemical
structuresUsed within the Pathway Tools in a substructure
searchCase is significant (lowercase for aromatic rings)Examples:
formate C(=O)Omalate OC(=O)CC(O)C(O)=O
For more information, see the Help facility
SRI InternationalBioinformaticsWhat’s in a Compound Page?
Sample (N-acetylglutamyl-phosphate)
Synonyms, empirical formula, MW, links
Structure
SMILES code
Pathways and reactions involving this compound
SRI InternationalBioinformaticsMiscellaneous Commands
History commandsAnswer-List commandsClone window commandFix window and unfix window commandsOther commands:
Print to file (makes a postscript) Help Preferences Exit
SRI InternationalBioinformaticsUser Preferences
ColorLayoutCompound windowReaction windowPathway windowHistory/Answer listReverting and saving user preferences
SRI InternationalBioinformaticsLab Exercises
Set up personal preferences for:
Color
Layout (set number of windows to 2)Save new preferencesPlay with settings for Compound, Reaction,
Pathway, and Overview windows.Choose settings for History/Answer List
preferences
SRI InternationalBioinformaticsLab Exercises
Retrieve compounds containing a formate groupRetrieve compounds adenine and uracil using
class query Retrieve reaction with EC# 5.3.1.9Retrieve all reactions in the class
sulfurtransferasesRetrieve all reactions involved in proline
biosynthesisRetrieve all reactions where glutamate appears on
left sidegenes coding for enzymes involved in the
degradation of short-chain fatty acids
SRI InternationalBioinformaticsLab Exercises
Retrieve all enzymes involved in purine biosynthesis
Retrieve all kinasesDisplay region spanning from 10 % - 20 % of E.
coli chromosome Display chromosomal region around gene aroADisplay a map showing all chaperone genes
SRI InternationalBioinformaticsLab Exercises
Retrieve all chaperone genesRetrieve gene aroAFind the glutamine biosynthesis pathway by
issuing each of the three types of queries in Pathway mode.