Pathway Studio™ is a trademark of Elsevier Inc.

Pathway Studio Plant

Finding mechanisms associated

with Rice Blast infection

2

RICE: A WORLD-WIDE ECONOMIC CROP

EVEN SMALL DISRUPTION IN SUPPLY ARE FELT

Rice: life sustaining, grown world wide

More than 20 fungal disease ravage rice;Rice Blast the worst

Recent advances have help; disease remains

a big challenge

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RICE BLAST CAUSES MAJOR CROP YIELD LOSES

UP TO 25% OF CROP CAN BE LOST

A wide range of physical damage In Japan, up to 25% of

yield lost to rice blast and

requires the extensive use

of fungicides.

Similar loses world wide.

Rice blast can destroy crop

in 10 days or less.

o

2 days

4 days6 days

8 days

4

Put rice plant picture

here

EXPLORE DISEASE AT MOLECULAR LEVEL

ASK CRITICAL QUESTIONS

The mechanisms

involved in blast

disease

resistance are

poorly understood

The objective of this study is to elucidate the mechanisms involved in plant defense against fungus.

Source data: GEO gene expression data set

Questions to be addressed:

• What genes change their activity the most?

• What pathways are activated or inhibited in response to rice blast?

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Experimental design

Microarray experiment

was performed for

three types of samples

(GDS3441):

Ribot C. et al. Susceptibility of

rice to the blast fungus,

Magnaporthe grisea. J Plant

Physiol 2008 Jan;165(1):114-24.

(PubMed ID: 17905473

ANALYSIS OF BLAST INFECTED RICE PLANTS

USE OF RICE SPECIFIC MICROARRAY DATA

1. Healthy rice leaves (rice cultivar Nipponbare)

2. Rice leaves, 4 days

after infection with M.

grisea FR13

Set up differential

expression analysis and

examine Day 4 vs control

Healthyleaf

3 days after

infection

4 days after

infection

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INTRODUCTION TO PLANT

DATABASE INCLUDES BOTH LITERATURE EXTRACTED RELATIONSHIPS

AS WELL AS MANUALLY CURATED DATA SETS

Literature Extracted Data

Vast and best quality relations

• >164,700 biological facts

• >240,700 PubMed Abstracts

• Over 76,000 full-text articles from Elsevier and

other publishers

Full text content from 31 Plant-specific

journals (18 Elsevier + 13 third party).

Significant additional full-text plant papers

from non-Plant journals

• Data for Arabidopsis, Corn and Rice

High quality content allowing best experimental data interpretation and model pathway building

DatabasesMammal, ChemEffect,

DiseaseFx,

Biological Relations

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TEXT MININGTHE NATURAL LANGUAGE PROCESSING TECHNOLOGY READS SCIENTIFIC LITERATURE AND

EXTRACTS DESCRIBED RELATIONS BETWEEN BIOLOGICAL CONCEPTS

PlantDatabase

Relation Extractionfrom literature

NaturalLanguage Processing

Literature Sources:• >240,700 PubMed Abstracts• >76,000 full-text articles from Elsevier

and other publishers

Biological Relations

8©2009 Ariadne. All Rights Reserved.

“In Arabidopsis, ethylene induces the expression of ERS1 and ETR2, but

represses that of ETR1.”

ethylene expression ERS1

ethylene expression ETR2

ethylene regulation ETR1

NLP: semantic triplets

Extracting relations

ethylene -> ERS1 relation: expression effect: positive organism: Arabidopsis

ethylene -> ETR2 relation: expression effect: positive organism: Arabidopsis

ethylene -> ETR1 relation: regulation effect: negative organism: Arabidopsis

IDENTIFIES “ENTITIES” AND “RELATIONSHIPS”PATHWAY STUDIO EXTRACTS SCIENTIFIC FINDINGS FROM THE LITERATURE

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INTRODUCTION TO PLANT

THE DATABASE INCLUDES BOTH LITERATURE EXTRACTED RELATIONSHIPS

AS WELL AS MANUALLY CURATED DATA SETS

Manually Curated Pathways and Ontologies

Curated Data in Plant

• >1250 curated metabolic and signaling

pathways

• Three ontologies:

Plant Ontology

Pathway Studio Ontology

Gene Ontology

>4800 predicted miRNA targets

High quality content allowing best experimental data interpretation and model pathway building

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EXPERIMENTAL DATA ANALYSIS

ACCESS DATABASE FOR PATHWAY BUILDING AND EXPERIMENTAL DATA MINING

• Streamlined approach to mapping

new organisms through similarity

to model organisms in

knowledgebase — speeding basic

and applied plant research

• Toggle between viewing two

experiment types on a pathway —

rapidly correlates experimental

findings in a single tool

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PATHWAY STUDIO PLANT WORKFLOW

GEO EXPRESSION DATA ANALYSIS STEPS

Summarize results

Import expression data

Enrichment Algorithm:pathways & cell processes

Review results

Use inferred pathways to explain results

Apply Build Pathway by Homology Tool

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START PAGE FOR PATHWAY STUDIO

TOOLS USED FOR THIS ANALYSIS

An Automated workflow

Import wizard

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IMPORT RICE EXPERIMENT

IMPORT WIZARD STREAMLINES PROCESS TO A FEW CLICKS

Import of

GDS3441 to

Pathway

Studio

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Wizard helps you to properly tag

columns in your experiment

IMPORT RICE EXPERIMENT

IMPORT WIZARD STREAMLINES PROCESS TO A FEW CLICKS

Import of

GDS3441 to

Pathway

Studio

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Select data type

IMPORT RICE EXPERIMENT

IMPORT WIZARD STREAMLINES PROCESS TO A FEW CLICKS

Import of

GDS3441 to

Pathway

Studio

16

Use one of suggested

map files for best

mapping results and

better experiment

analysis

IMPORT RICE EXPERIMENT

IMPORT WIZARD STREAMLINES PROCESS TO A FEW CLICKS

Import of

GDS3441 to

Pathway

Studio

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IMPORT RICE EXPERIMENT

IMPORT WIZARD STREAMLINES PROCESS TO A FEW CLICKS

Import of

GDS3441 to

Pathway

Studio

Your experiment is

now imported and you

can analyze it using

Pathway Studio

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EXPERIMENT SUMMARY ANALYSIS TOOL

1. Select an

experiment

2. Select differential

samples

3. Generates 8

reports in 3

minutes or less

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FIND THE TOP MOST CHANGING GENES IN DATA SET

MORE DETAILS ON IMMUNE RESPONSE

Lists of top

up- and down-

regulated

genes allows

you to focus

on particular

proteins.

Genes associated with plant defense

in the top up-regulated genes

include:

• 2 chitinases - enzymes capable of

degrading fungal cell wall;

• A rice homolog of WRKY18 (Arabidopsis)

which is widely involved in plant’s

response to stress

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CELL PROCESSES AFFECTED BY RICE BLAST

RICE IMMUNE SYSTEM IS ACTIVATED

Look at

affected cell

processes.

8 out of 10

results are

related to plant

immune and

stress response.Red indicates up-regulated

genes in data set.

Blue indicates down-regulated genes in data set

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PATHWAYS AFFECTED BY RICE BLAST

Pathways

involved with

biosynthesis of

cell wall

components

suggest

protective

mechanism

induced in rice

plant.

MORE DETAILS ON IMMUNE RESPONSE

Biosynthesis of salicylate and chorismate

(salicylate precursor) are highly relevant

plant immune response pathways.

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INVESTIGATE

SALICYLATE

SIGNALING PATHWAY

Summarize results

Import expression data

Enrichment Algorithm:pathways & cell

processes

Review results

Use inferred pathways to explain results

Apply Build Pathway by Homology Tool

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ARABIDOPSIS SALICYLATE SIGNALING PATHWAY

WELL-STUDIED MODEL ORGANISM

Salicylate Pathway:

One of over 1100 curated

pathways

How can we overlay rice

data onto an Arabidopsis

salicylate signaling

pathway?

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BUILD PATHWAY BY HOMOLOGY

LEVERAGING ARABIDOPSIS DATA TO GAIN INSIGHT INTO RICE MECHANISMS

Arabidopsis proteins and literature extracted relations

Arabidopsis proteins

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BUILD PATHWAY BY HOMOLOGY

LEVERAGING ARABIDOPSIS DATA TO GAIN INSIGHT INTO RICE MECHANISMS

Arabidopsis proteins and literature extracted relations

Identify rice orthologs

Arabidopsis proteins rice proteins

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BUILD PATHWAY BY HOMOLOGY

LEVERAGING ARABIDOPSIS DATA TO GAIN INSIGHT INTO RICE MECHANISMS

Arabidopsis proteins and literature extracted relations

Some relations may already exist for the rice orthologs

Arabidopsis proteins rice proteins

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BUILD PATHWAY BY HOMOLOGY

LEVERAGING ARABIDOPSIS DATA TO GAIN INSIGHT INTO RICE MECHANISMS

Arabidopsis proteins and literature extracted relations

Some relations may already exist for the rice orthologs

Complete the pathway by INFERRED Arabidopsis relations

Arabidopsis proteins rice proteins rice proteins

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CREATE PATHWAY BY HOMOLOGY

FROM ARABIDOPSIS TO RICE IN MINUTES

CREATE PATHWAY BY

HOMOLOGY TOOL

Uses Arabidopsis information

to infer Rice pathways,

entities, functions and

interactions in rice.

Use Arabidopsis Salicylate

signaling pathway

Click on Arabidopsis pathway to open

menu.Select source organism and then target organism to

create new pathway.

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FROM ARABIDOPSIS TO RICE

SALICYLATE SIGNALING PATHWAY

From Arabidopsis..

..to Inferred rice

pathway

Hypothetical relations connect

homologous proteins

Proteins from Arabidopsis that have homology with rice proteins were replaced with rice proteins.

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RICE SALICYLIC ACID SIGNALING 4 DAYS AFTER INFECTION

EXPERIMENTAL DATA OVERLAY

Inferred salicylic acid

signaling pathway helps

to explain observed

changes in gene

expressionOsNPR1

OsCH6

OsPR1b

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Can we explain changes in metabolism by salicylate signaling?

Up-regulated members of cell wall biosynthesis pathway that are

downstream from salicylate signaling pathway are the link

LINKING RICE SALICYLATE SIGNALING TO METABOLIC CHANGES

Salicylatebiosynthesis

Salicylate signaling

Cell wall components

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OsSIPK, OsNPR1 and

OsPAL1are potential

mediators linking

salicylate signaling

to cell wall

biosynthesis.

LINKING RICE SALICYLATE SIGNALING TO METABOLIC CHANGES

Rice homolog of

PAL1

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From Experimental Summary Analysis Tool:

Identified WRKY18 as a factor of susceptibility to blast.

Found cell processes and metabolic pathways affected by blast:

activation of disease and stress responses, cell wall biosynthesis and

salicylate production

Pathway Studio Plant provided the ability to reconstruct key

regulatory pathways for rice

Found OsSIPK, OsNPR1 and PAL1, as mediators between salicylate

signaling cascade and cell wall biosynthesis.

Built a mechanistic model explaining increased expression of chitinase 6,

an important player of plant defense.

SUMMARY OF EXPERIMENTAL FINDINGS

USING PATHWAY STUDIO PLANT

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Thank you

For questions & demonstrations:

elsevier.com/on-line/pathway-studio