1. Volume 2, Issue 5, Pages 1067-1083 (September 2009)
Analysis of Transcriptome Changes Induced by Ptr ToxA in Wheat Provides Insights into the Mechanisms of Plant Susceptibility 
Pandelova Iovanna , Betts Melania F. , Manning Viola A. , Wilhelm Larry J. , Mockler Todd C. , Ciuffetti Lynda M.  
Molecular Plant 
Volume 2, Issue 5, Pages (September 2009)
DOI: /mp/ssp045
Copyright © 2009 The Authors. All rights reserved. Terms and Conditions

2. Figure 1
ToxA-Induced Symptom Development and Regulation of Probesets in ToxA-Sensitive Leaves over Time.
(A) Bioassay of leaves treated with H2O (–) or 1 μM ToxA (+) and collected at 3, 9, 14, and 48 h post infiltration (hpi). Dots demarcate treatment area.
(B) Statistically significant differentially expressed probesets in ToxA- vs H2O-treated leaves at 3, 9, and 14 hpi with increased (gray) or decreased (white) mRNA levels. Number of probesets is indicated within each bar.
Molecular Plant 2009 2, DOI: ( /mp/ssp045)
Copyright © 2009 The Authors. All rights reserved. Terms and Conditions

3. Figure 2 ToxA Effect on Global Transcriptional Reprogramming.
Statistically significant dataset was grouped by broad GO categories (by TAIR). Bars represent the number of up- (gray) and down-regulated (white) probesets. Panels represent transcriptional changes for cellular components (A), molecular function (B), and biological processes (C) in ToxA-sensitive leaves harvested at 3, 9, and 14 h post infiltration.
Molecular Plant 2009 2, DOI: ( /mp/ssp045)
Copyright © 2009 The Authors. All rights reserved. Terms and Conditions

4. Figure 3
ToxA-Induced Regulation of Different Receptor and Receptor-Associated Families over Time.
Bars represent the number of up- (gray) and down-regulated (white) genes. Numbers in bars represent the number of corresponding probesets. Receptor family names to the right of each bar include: wall-associated kinase (WAK), SNAREs (including syntaxin and v-SNARE), receptor kinase (includes other receptor-like kinases), brassinosteroid-associated (BRI1-A) receptor kinase. Serine-threonine protein kinase receptor precursor (Ser/Thr kinase). S/R represents number of significantly regulated probesets (S) vs. probesets for their families represented on the chip (R). Range of fold change is presented for up- and down-regulated probesets at each time point. Non-significant changes are indicated as n/s.
Molecular Plant 2009 2, DOI: ( /mp/ssp045)
Copyright © 2009 The Authors. All rights reserved. Terms and Conditions

5. Figure 4
ToxA-Induced Regulation of Genes Involved in Phenylpropanoid Pathway over Time.
Bars represent the number of up- (gray) and down-regulated (white) genes. Numbers in bars represent the number of corresponding probesets. Corresponding protein family names to the right of each bar include: phenylalanine amonia lyase (PAL), trans-cinnamate 4-monooxygenase (C4H), 4-coumarate–CoA ligase (4CCoAL), caffeoyl-CoA O-methyltransferase (CCoAM), cinnamyl alcohol dehydrogenase (CAD). S/R represents number of significantly regulated probesets (S) vs. probesets for their families represented on the chip (R). Range of fold change is presented for up- and down-regulated probesets at each time point. Non-significant changes are indicated as n/s.
Molecular Plant 2009 2, DOI: ( /mp/ssp045)
Copyright © 2009 The Authors. All rights reserved. Terms and Conditions

6. Figure 5
ToxA-Induced Regulation of Genes Involved in Jasmonic Acid Synthesis over Time.
Bars represent the number of up- (gray) and down-regulated (white) genes. Numbers in bars represent the number of corresponding probesets. Corresponding protein family names to the right of each bar include: phospholypase C and D (PL), lypoxygenase (LOX), allene oxide synthase (AOS), allene oxide cyclase (AOC), 12-oxophytodienoate reductase (OPDAR). S/R represents number of significantly regulated probesets (S) vs. probe sets for their families represented on the chip (R). Range of fold change is presented for up- and down-regulated probe sets at each time point. Non-significant changes are indicated as n/s.
Molecular Plant 2009 2, DOI: ( /mp/ssp045)
Copyright © 2009 The Authors. All rights reserved. Terms and Conditions

7. Figure 6
ToxA-Induced Regulation of Different Groups of Pathogenesis-Related (PR) Genes over Time.
Bars represent the number of up- (gray) and down-regulated (white) genes. Numbers in bars represent the number of corresponding probesets. Corresponding protein family names to the right of each bar include: 1,3-β-glucanase (PR-2), chitinase (PR-4), thaumatin-like (PR-5). S/R represents number of significantly regulated probesets (S) vs. probesets for their families represented on the chip (R). Range of fold change is presented for up- and down-regulated probe sets at each time point. Non-significant changes are indicated as n/s.
Molecular Plant 2009 2, DOI: ( /mp/ssp045)
Copyright © 2009 The Authors. All rights reserved. Terms and Conditions

8. Figure 7
ToxA-Induced Regulation of Genes Involved in Photosynthesis over Time.
Bars represent the number of up- (gray) and down-regulated (white) genes. Numbers in bars represent the number of corresponding probesets. Corresponding protein family names to the right of each bar include: chlorophyll a/b binding proteins (Chl a/b), and photosystems I (PS I) and II (PS II) and ferredoxin (FDX). S/R represents number of significantly regulated probesets (S) vs. probesets for their families represented on the chip (R). Range of fold change is presented for up- and down-regulated probesets at each time point. Non-significant changes are indicated as n/s.
Molecular Plant 2009 2, DOI: ( /mp/ssp045)
Copyright © 2009 The Authors. All rights reserved. Terms and Conditions

9. Figure 8
ToxA-Induced Regulation of Genes Involved in Oxidative Stress over Time.
Bars represent the number of up- (gray) and down-regulated (white) genes. Numbers in bars represent the number of corresponding probesets. Corresponding protein family names to the right of each bar include: glutathione-s-transferase (GST), phospholipid hydroperoxide glutathione peroxidase 1 (GPX), ascorbate peroxidase (APX), peroxidase (PX), superoxide dismutase (SOD). S/R represents number of significantly regulated probesets (S) vs. probesets for their families represented on the chip (R). Range of fold change is presented for up- and down-regulated probesets at each time point. Non-significant changes are indicated as n/s.
Molecular Plant 2009 2, DOI: ( /mp/ssp045)
Copyright © 2009 The Authors. All rights reserved. Terms and Conditions

10. Figure 9 Microarray Validation Results by Selected Probesets.
(A) Expression patterns were validated by RT–PCR. Experiments were repeated at least two times, with similar results, for each probeset, using two biological replicates.
(B) Graphs represent expression patterns of corresponding probesets for mock- (open circle) and ToxA-treated (black circle) leaves. Data represent mean and standard deviation of microarray signal intensities from three biological replicates.
Molecular Plant 2009 2, DOI: ( /mp/ssp045)
Copyright © 2009 The Authors. All rights reserved. Terms and Conditions