Navigator - Bioinformatics Research Group at SRI International

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2 Οκτ 2013 (πριν από 4 χρόνια και 1 μήνα)

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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

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Introduction


Navigator 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

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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

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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)

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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


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Indirect Queries




Related objects



Objects are clickable



Objects are color
-
coded by type

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History List




Backward history



Forward history



Select 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 in mnemonic form



Click on citation


go to citations at bottom of
page



Click there, go to PubMed ref, if available

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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

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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

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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 the reaction is involved in



Place 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



Enzymatic reaction frames


how
this

protein
carries out
that

reaction (bridging the two)



Evidence codes

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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


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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

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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)

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Compound Mode Commands


Search compound by name



Search compound by substring



Search by SMILES (structure)



Search by class



Advanced search

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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


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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

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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

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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 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


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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


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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


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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.

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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