Using inferred pathways relations to find mechanisms associated with a plant disease Rice blast is a fungal infection that can devastate growing crops within 7-10 days. It can survive on seeds or in soil, subsequent crops can be infected. Despite all attempts to fight this disease, rice blast still ravages yields. The use of fungicides extends the plant’s useful life, however, blast overcomes resistance within 1 to 2 growing seasons. Analysis of rice response to blast infection can shed light on plant immunity and improve breeding decisions. This webinar will demonstrate how the utilization of Arabidopsis data in Pathway Studio helps further the understanding of rice blast defense mechanisms.

1. Pathway Studio™ is a trademark of Elsevier Inc.
Pathway Studio Plant
Finding mechanisms associated
with Rice Blast infection

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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

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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
Healthy
leaf
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
Databases
Mammal, ChemEffect,
DiseaseFx,
Biological Relations

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TEXT MINING
THE NATURAL LANGUAGE PROCESSING TECHNOLOGY READS SCIENTIFIC LITERATURE AND
EXTRACTS DESCRIBED RELATIONS BETWEEN BIOLOGICAL CONCEPTS
Plant
Database
Relation Extraction
from literature
Natural
Language
Processing
Literature Sources:
• >240,700 PubMed Abstracts
• >76,000 full-text articles from Elsevier
and other publishers
Biological Relations

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©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

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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
Salicylate
biosynthesis
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