The Pathway/Genome Navigator

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

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

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

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 don’t know an exact name Searches that are specific to object type

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

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

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

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

Select Current Organism Click on “change” Under Quick Search button Bottom of Search menu Bottom of Tools menu Select by typing or clicking

Organism Pages Tools -> Reports -> Summary statistics PGDB authors, statistics

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)

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

Shared Display Characteristics Gene-Reaction schematic Citations and comments Database Links Classes

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

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

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

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

Desktop Mode

Desktop Mode Linux/PC, Windows/PC, Macintosh

Desktop Window Layout One Large Window Several Panes: Display pane Command menu LISP listener

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

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 you’re over, what you can do)

Queries with Multiple Answers Results in form of a menu to: select one some all Answer List Next Answer

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

Select Current Organism From All Organisms Page Through organism selector

Pathway Mode Commands Search by pathway name Search by substring Search by class Search by substrates (can pick role in pathway)

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

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

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)

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

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

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

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 Transcription Unit Frame? 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)

Compound Mode Commands Search compound by name Search compound by substring Search by SMILES (structure) Search by class Advanced search

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

What’s in a Compound Frame? Sample (N-acetylglutamyl-phosphate) Synonyms, empirical formula, MW, links Structure SMILES code Pathways and reactions involving this compound

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 history Forward history Select from history

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

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

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

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

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

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.

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