The Pathway/Genome Navigator

(These slides are a guide as you experiment with the Navigator)

Pathway/Genome Navigator – topics

Getting started with the NavigatorOrganism pagesQueries in generalObject displays and queriesMiscellaneous commandsUser preferencesLab exercises

Introduction

Navigator runs both on the desktop and on the web

The desktop version generally has more capabilities, but each has unique features

Desktop Mode -- Introduction

Desktop Layout

One Large Window

Several Panes: Display pane Command menu LISP listener

Desktop 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)

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

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

History List

Backward history

Forward history

Select from history

Writing Complex Queries

Web Search Advanced

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

Overview of Object Displays

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, rxnsLinks proteins with shared reactions

ArgDLinks 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 Gene page: For coli, we added links to coli-specific sites

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

Menu Categories

PathwayReactionProtein(RNA)GeneCompound

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 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

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 TU 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 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

What’s in a compound frame?

Sample (N-acetylglutamyl-phosphate)

Synonyms, empirical formula, MW, links

Structure (you can add these in editors)

SMILES code

Pathways and reactions involving this compound

Miscellaneous Commands

History commandsAnswer-List commandsClone window commandFix window and unfix window commandsOther commands:

Print to file (makes a postscript) Help Preferences Exit

User Preferences

ColorLayoutCompound windowReaction windowPathway windowHistory/Answer listReverting and saving user preferences

Lab Exercises – Desktop Version

Lab 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

Desktop Lab 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

Desktop Lab 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

Desktop Lab Exercises

Retrieve all chaperone genesRetrieve gene aroAFind the glutamine biosynthesis pathway by

issuing each of the three types of queries in Pathway mode.

Desktop Lab Exercises

Clone windowNavigate in the cloned windowSet preferences so Navigator displays 2 windowsNavigate by clicking on live objectsFix WindowNavigate in unfixed windowFix second window and then click on live object

The Web Interface: BioCyc

Ron Caspi

Help is One Click Away!

The Web Account System

The Web Account System

Creating a web account enables you to:

Save Object Groups

Define page formatting preferences

Define Overview layout preferences

Save organism groups for comparative analysis

Save Organism Groups with Web Accounts

Note the My Lists tab on the multi-organism selector for comparative analyses.

When you perform comparative analyses, you can easily save groups of organisms for re-using at a later time.

Define a Favorite Database with Web Accounts

If you create a web

account, you can define

a favorite database that

will be opened by

default when you login

Searching the Database

Why the Need for Dedicated Search Tools

Search BioCyc for “L-arginine”

2080 results

Need to have specific tools for finding exactly

what we search for.

BioCyc Searches

Multiple searches available for finding information in different ways

The easiest searches to use are fairly coarse

Start by selecting database to search

Simplest search: Quick Search At upper right of most pages

Selecting the Database

You can only search one database at a time*!

* With the exception of Google searches

Click on word “change” under Search menu or under Quick

Search button

In resulting selector, choose a PGDB

Start typing a word in organism name

Click on letter to navigate to organisms starting with that letter

Click a frequently used PGDB Select by Taxonomy

All subsequent searches will apply to that database

The Quick Search Box What can you type here:

Gene names (dnaA ) Compound name (L-lysine) Pathway name (peptidoglycan biosynthesis) Reaction name (lysine decarboxylase) Protein name (peptidase) EC number (1.3.1.26) Organism name (Escherichia coli) Frame ID (CPLX-8024) GO term (0006086) Links to other databases (O33998) An exact term using the format (Peptidase D search:exact) Limited term (hydrogen type:compound)

What doesn’t work: Exact text using the Google format (“peptidase D”)

Quick Search Results

Results are divided into multiple categories

Examples of searches performed by users of the BioCyc website:

Successful Unsuccessful Ascorbate pheV EC 3.4.17.5 Transmembrane helix

6 Sigma factor 3.4.24.B11 Polysulfide reductase ABC cobalt transporter Entner-Doudoroff pathway affinity of DnaACyanobacteria DnaA

A simple auto-correction mechanism tries to correct typos. For example, searching for “sacrosine” will find “sarcosine”.

Quick Gene Search

Useful when only interested in genes.

For example, compare the results when searching for “dnaA” by using the Quick Search and Gene Search buttons.

The Search Menu

Search Menu Object-specific searches Advanced search Ontologies search Google search BLAST search Search of full-text articles (EcoCyc only)

Google This Site

The BioCyc site is indexed by Google

You can launch a Google text search from:

1. Search → Google This Site

2. The alternative searches box that appears on Quick Search results pages

Object-Specific Searches

The first four items in the search menu provide a medium-level search interface against single types of objects

Use of filtering

Click on triangles at the left to expand or hide filters

Note that if a filter is hidden it will not be used in a

search

Compound Search

List All buttons – quick way to get complete listsExamples for compound searching:

Search Genes/Proteins/RNAs

List All buttons – quick way to get complete listsExtensive filtering options

Search Pathways

Advanced Search

The BioVelo query languageSAQP: Structured Advanced Query Page

Permits the definition of complex searches without mastering BioVelo.

To learn more about the advanced query interface, see online

documentation.

Sequence Search by BLAST

Nothing unusual here – a regular BLAST interface that permits BLASTing sequences against BioCyc PGDBs.

The results are linked to the PGDB gene/protein pages

The desktop version of Pathway Tools allows definition of growth media, gene knockout growth information, and growth data for phenotype microarray plates.

Growth Media and Phenotype

EcoCyc-Specific Searches: Growth MediaSearch for growth media based on:

namecompounds presentcompounds not presentobserved growth

EcoCyc-Specific Searches: Textpresso

Mining E. coli literature poses special challenges – because almost every molecular biology paper references E. coli

The solution – EcoCyc Textpresso! An E. coli only collection of literature

30,000 full-text articles and 6,500 abstracts.

Full text literature searches

Results presented at bottom of page

Web Version Lab Exercises

Web Lab Exercises

In EcoCyc:

Retrieve gene aroARetrieve all kinasesRetrieve all chaperone genes using two different

approachesRetrieve all membrane proteins that cite an article

by GrossRetrieve all genes whose product interacts with

ppGpp as a regulator or cofactor

Web Lab Exercises

In MetaCyc:

Retrieve reaction with EC# 5.3.1.9Retrieve compounds adenine and uracil using

ontology search Retrieve all reactions involving glutamate as a

substrateFind genes coding for enzymes involved in the

degradation of short-chain fatty acidsFind all pathways involved in degradation of

arginine