Differential Coexpression Analysis Reveals Extensive Rewiring of Arabidopsis Gene Coexpression in Response to Pseudomonas syringae Infection
Abstract
Plant defense responses to pathogens involve massive transcriptional reprogramming. Recently, differential coexpression analysis has been developed to study the rewiring of gene networks through microarray data, which is becoming an important complement to traditional differential expression analysis. Using time-series microarray data of Arabidopsis thaliana infected with Pseudomonas syringae, we analyzed Arabidopsis defense responses to P. syringae through differential coexpression analysis. Overall, we found that differential coexpression was a common phenomenon of plant immunity. Genes that were frequently involved in differential coexpression tend to be related to plant immune responses. Importantly, many of those genes have similar average expression levels between normal plant growth and pathogen infection but have different coexpression partners. By integrating the Arabidopsis regulatory network into our analysis, we identified several transcription factors that may be regulators of differential coexpression during plant immune responses. We also observed extensive differential coexpression between genes within the same metabolic pathways. Several metabolic pathways, such as photosynthesis light reactions, exhibited significant changes in expression correlation between normal growth and pathogen infection. Taken together, differential coexpression analysis provides a new strategy for analyzing transcriptional data related to plant defense responses and new insights into the understanding of plant-pathogen interactions.
- Authors:
-
- China Agricultural Univ., Beijing (China). College of Biological Sciences. State Key Lab. of Agrobiotechnology
- China Agricultural Univ., Beijing (China). College of Biological Sciences. State Key Lab. of Agrobiotechnology; Brookhaven National Lab. (BNL), Upton, NY (United States). Biology Dept.
- Publication Date:
- Research Org.:
- Brookhaven National Laboratory (BNL), Upton, NY (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
- OSTI Identifier:
- 1624864
- Grant/Contract Number:
- SC0012704
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Scientific Reports
- Additional Journal Information:
- Journal Volume: 6; Journal Issue: 1; Journal ID: ISSN 2045-2322
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Science & Technology - Other Topics
Citation Formats
Jiang, Zhenhong, Dong, Xiaobao, Li, Zhi-Gang, He, Fei, and Zhang, Ziding. Differential Coexpression Analysis Reveals Extensive Rewiring of Arabidopsis Gene Coexpression in Response to Pseudomonas syringae Infection. United States: N. p., 2016.
Web. doi:10.1038/srep35064.
Jiang, Zhenhong, Dong, Xiaobao, Li, Zhi-Gang, He, Fei, & Zhang, Ziding. Differential Coexpression Analysis Reveals Extensive Rewiring of Arabidopsis Gene Coexpression in Response to Pseudomonas syringae Infection. United States. https://doi.org/10.1038/srep35064
Jiang, Zhenhong, Dong, Xiaobao, Li, Zhi-Gang, He, Fei, and Zhang, Ziding. Mon .
"Differential Coexpression Analysis Reveals Extensive Rewiring of Arabidopsis Gene Coexpression in Response to Pseudomonas syringae Infection". United States. https://doi.org/10.1038/srep35064. https://www.osti.gov/servlets/purl/1624864.
@article{osti_1624864,
title = {Differential Coexpression Analysis Reveals Extensive Rewiring of Arabidopsis Gene Coexpression in Response to Pseudomonas syringae Infection},
author = {Jiang, Zhenhong and Dong, Xiaobao and Li, Zhi-Gang and He, Fei and Zhang, Ziding},
abstractNote = {Plant defense responses to pathogens involve massive transcriptional reprogramming. Recently, differential coexpression analysis has been developed to study the rewiring of gene networks through microarray data, which is becoming an important complement to traditional differential expression analysis. Using time-series microarray data of Arabidopsis thaliana infected with Pseudomonas syringae, we analyzed Arabidopsis defense responses to P. syringae through differential coexpression analysis. Overall, we found that differential coexpression was a common phenomenon of plant immunity. Genes that were frequently involved in differential coexpression tend to be related to plant immune responses. Importantly, many of those genes have similar average expression levels between normal plant growth and pathogen infection but have different coexpression partners. By integrating the Arabidopsis regulatory network into our analysis, we identified several transcription factors that may be regulators of differential coexpression during plant immune responses. We also observed extensive differential coexpression between genes within the same metabolic pathways. Several metabolic pathways, such as photosynthesis light reactions, exhibited significant changes in expression correlation between normal growth and pathogen infection. Taken together, differential coexpression analysis provides a new strategy for analyzing transcriptional data related to plant defense responses and new insights into the understanding of plant-pathogen interactions.},
doi = {10.1038/srep35064},
journal = {Scientific Reports},
number = 1,
volume = 6,
place = {United States},
year = {Mon Oct 10 00:00:00 EDT 2016},
month = {Mon Oct 10 00:00:00 EDT 2016}
}
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Works referenced in this record:
The plant immune system
journal, November 2006
- Jones, Jonathan D. G.; Dangl, Jeffery L.
- Nature, Vol. 444, Issue 7117
Comparing signaling mechanisms engaged in pattern-triggered and effector-triggered immunity
journal, August 2010
- Tsuda, Kenichi; Katagiri, Fumiaki
- Current Opinion in Plant Biology, Vol. 13, Issue 4
Transcription Dynamics in Plant Immunity
journal, August 2011
- Moore, John W.; Loake, Gary J.; Spoel, Steven H.
- The Plant Cell, Vol. 23, Issue 8
Biological context networks: a mosaic view of the interactome
journal, January 2006
- Rachlin, John; Cohen, Dikla Dotan; Cantor, Charles
- Molecular Systems Biology, Vol. 2, Issue 1
Deciphering the Arabidopsis Floral Transition Process by Integrating a Protein-Protein Interaction Network and Gene Expression Data
journal, June 2010
- He, Fei; Zhou, Yuan; Zhang, Ziding
- Plant Physiology, Vol. 153, Issue 4
Molecular Signatures in Arabidopsis thaliana in Response to Insect Attack and Bacterial Infection
journal, March 2013
- Barah, Pankaj; Winge, Per; Kusnierczyk, Anna
- PLoS ONE, Vol. 8, Issue 3
Discovery of Core Biotic Stress Responsive Genes in Arabidopsis by Weighted Gene Co-Expression Network Analysis
journal, March 2015
- Amrine, Katherine C. H.; Blanco-Ulate, Barbara; Cantu, Dario
- PLOS ONE, Vol. 10, Issue 3
Construction and comparison of gene co-expression networks shows complex plant immune responses
journal, January 2014
- Leal, Luis Guillermo; López, Camilo; López-Kleine, Liliana
- PeerJ, Vol. 2
Expression-based network biology identifies immune-related functional modules involved in plant defense
journal, January 2014
- Tully, Joel P.; Hill, Aubrey E.; Ahmed, Hadia MR
- BMC Genomics, Vol. 15, Issue 1
Revealing Shared and Distinct Gene Network Organization in Arabidopsis Immune Responses by Integrative Analysis
journal, January 2015
- Dong, Xiaobao; Jiang, Zhenhong; Peng, You-Liang
- Plant Physiology, Vol. 167, Issue 3
Network-Based Comparative Analysis of Arabidopsis Immune Responses to Golovinomyces orontii and Botrytis cinerea Infections
journal, January 2016
- Jiang, Zhenhong; Dong, Xiaobao; Zhang, Ziding
- Scientific Reports, Vol. 6, Issue 1
Network Modeling to Understand Plant Immunity
journal, August 2014
- Windram, Oliver; Penfold, Christopher A.; Denby, Katherine J.
- Annual Review of Phytopathology, Vol. 52, Issue 1
Toward a systems understanding of plant–microbe interactions
journal, August 2014
- Mine, Akira; Sato, Masanao; Tsuda, Kenichi
- Frontiers in Plant Science, Vol. 5
Systems understanding of plant–pathogen interactions through genome-wide protein–protein interaction networks
journal, January 2016
- Li, Hong; Zhang, Ziding
- Frontiers of Agricultural Science and Engineering, Vol. 3, Issue 2
From ‘differential expression’ to ‘differential networking’ – identification of dysfunctional regulatory networks in diseases
journal, July 2010
- de la Fuente, Alberto
- Trends in Genetics, Vol. 26, Issue 7
Beyond modules and hubs: the potential of gene coexpression networks for investigating molecular mechanisms of complex brain disorders: Beyond modules and hubs
journal, December 2013
- Gaiteri, C.; Ding, Y.; French, B.
- Genes, Brain and Behavior, Vol. 13, Issue 1
Functional Analysis and Characterization of Differential Coexpression Networks
journal, August 2015
- Hsu, Chia-Lang; Juan, Hsueh-Fen; Huang, Hsuan-Cheng
- Scientific Reports, Vol. 5, Issue 1
Genome-wide coexpression dynamics: Theory and application
journal, December 2002
- Li, K. -C.
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 26
Dissection of Regulatory Networks that Are Altered in Disease via Differential Co-expression
journal, March 2013
- Amar, David; Safer, Hershel; Shamir, Ron
- PLoS Computational Biology, Vol. 9, Issue 3
DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules
journal, January 2010
- Tesson, Bruno M.; Breitling, Rainer; Jansen, Ritsert C.
- BMC Bioinformatics, Vol. 11, Issue 1
DiffCorr: An R package to analyze and visualize differential correlations in biological networks
journal, April 2013
- Fukushima, Atsushi
- Gene, Vol. 518, Issue 1
DCGL v2.0: An R Package for Unveiling Differential Regulation from Differential Co-expression
journal, November 2013
- Yang, Jing; Yu, Hui; Liu, Bao-Hong
- PLoS ONE, Vol. 8, Issue 11
Exploring Tomato Gene Functions Based on Coexpression Modules Using Graph Clustering and Differential Coexpression Approaches
journal, February 2012
- Fukushima, Atsushi; Nishizawa, Tomoko; Hayakumo, Mariko
- Plant Physiology, Vol. 158, Issue 4
Differential coexpression analysis using microarray data and its application to human cancer
journal, October 2005
- Choi, J. K.; Yu, U.; Yoo, O. J.
- Bioinformatics, Vol. 21, Issue 24
A Differential Wiring Analysis of Expression Data Correctly Identifies the Gene Containing the Causal Mutation
journal, May 2009
- Hudson, Nicholas J.; Reverter, Antonio; Dalrymple, Brian P.
- PLoS Computational Biology, Vol. 5, Issue 5
Extensive Decoupling of Metabolic Genes in Cancer
journal, May 2015
- Reznik, Ed; Sander, Chris
- PLOS Computational Biology, Vol. 11, Issue 5
Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis
journal, June 2016
- He, Fei; Yoo, Shinjae; Wang, Daifeng
- The Plant Journal, Vol. 86, Issue 6
Chloroplasts play a central role in plant defence and are targeted by pathogen effectors
journal, June 2015
- de Torres Zabala, Marta; Littlejohn, George; Jayaraman, Siddharth
- Nature Plants, Vol. 1, Issue 6
Novel JAZ co‐operativity and unexpected JA dynamics underpin A rabidopsis defence responses to P seudomonas syringae infection
journal, October 2015
- Torres Zabala, Marta; Zhai, Bing; Jayaraman, Siddharth
- New Phytologist, Vol. 209, Issue 3
Transcriptional Dynamics Driving MAMP-Triggered Immunity and Pathogen Effector-Mediated Immunosuppression in Arabidopsis Leaves Following Infection with Pseudomonas syringae pv tomato DC3000
journal, November 2015
- Lewis, Laura A.; Polanski, Krzysztof; de Torres-Zabala, Marta
- The Plant Cell, Vol. 27, Issue 11
NCBI GEO: archive for functional genomics data sets—update
journal, November 2012
- Barrett, Tanya; Wilhite, Stephen E.; Ledoux, Pierre
- Nucleic Acids Research, Vol. 41, Issue D1
The microRNA miR393 re-directs secondary metabolite biosynthesis away from camalexin and towards glucosinolates: miR393 promotes glucosinolate biosynthesis
journal, June 2011
- Robert-Seilaniantz, Alexandre; MacLean, Dan; Jikumaru, Yusuke
- The Plant Journal, Vol. 67, Issue 2
Arabidopsis Defense against Botrytis cinerea : Chronology and Regulation Deciphered by High-Resolution Temporal Transcriptomic Analysis
journal, September 2012
- Windram, Oliver; Madhou, Priyadharshini; McHattie, Stuart
- The Plant Cell, Vol. 24, Issue 9
The Gene Ontology (GO) database and informatics resource
journal, January 2004
- Gene Ontology Consortium,
- Nucleic Acids Research, Vol. 32, Issue 90001
The U-Box Protein CMPG1 Is Required for Efficient Activation of Defense Mechanisms Triggered by Multiple Resistance Genes in Tobacco and Tomato
journal, March 2006
- González-Lamothe, Rocío; Tsitsigiannis, Dimitrios I.; Ludwig, Andrea A.
- The Plant Cell, Vol. 18, Issue 4
maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments
journal, February 2006
- Conesa, A.; Nueda, M. J.; Ferrer, A.
- Bioinformatics, Vol. 22, Issue 9
Transcriptional networks in plant immunity
journal, January 2015
- Tsuda, Kenichi; Somssich, Imre E.
- New Phytologist, Vol. 206, Issue 3
AGRIS: the Arabidopsis Gene Regulatory Information Server, an update
journal, November 2010
- Yilmaz, A.; Mejia-Guerra, M. K.; Kurz, K.
- Nucleic Acids Research, Vol. 39, Issue Database
PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors
journal, October 2013
- Jin, Jinpu; Zhang, He; Kong, Lei
- Nucleic Acids Research, Vol. 42, Issue D1
Discerning static and causal interactions in genome-wide reverse engineering problems
journal, May 2008
- Zampieri, Mattia; Soranzo, Nicola; Altafini, Claudio
- Bioinformatics, Vol. 24, Issue 13
Differential co-expression and regulation analyses reveal different mechanisms underlying major depressive disorder and subsyndromal symptomatic depression
journal, April 2015
- Xu, Fan; Yang, Jing; Chen, Jin
- BMC Bioinformatics, Vol. 16, Issue 1
An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors
journal, March 2015
- Jin, Jinpu; He, Kun; Tang, Xing
- Molecular Biology and Evolution, Vol. 32, Issue 7
AthaMap-assisted transcription factor target gene identification in Arabidopsis thaliana
journal, January 2010
- Bulow, L.; Brill, Y.; Hehl, R.
- Database, Vol. 2010, Issue 0
Coronatine Promotes Pseudomonas syringae Virulence in Plants by Activating a Signaling Cascade that Inhibits Salicylic Acid Accumulation
journal, June 2012
- Zheng, Xiao-yu; Spivey, Natalie Weaver; Zeng, Weiqing
- Cell Host & Microbe, Vol. 11, Issue 6
Crosstalk between abiotic and biotic stress responses: a current view from the points of convergence in the stress signaling networks
journal, August 2006
- Fujita, Miki; Fujita, Yasunari; Noutoshi, Yoshiteru
- Current Opinion in Plant Biology, Vol. 9, Issue 4
Identification of a novel gene HYS1/CPR5 that has a repressive role in the induction of leaf senescence and pathogen-defence responses in Arabidopsis thaliana
journal, February 2002
- Yoshida, Satoko; Ito, Masaki; Nishida, Ikuo
- The Plant Journal, Vol. 29, Issue 4
Photosynthesis, photorespiration, and light signalling in defence responses
journal, January 2012
- Kangasjarvi, S.; Neukermans, J.; Li, S.
- Journal of Experimental Botany, Vol. 63, Issue 4
Phytoalexins in defense against pathogens
journal, February 2012
- Ahuja, Ishita; Kissen, Ralph; Bones, Atle M.
- Trends in Plant Science, Vol. 17, Issue 2
Regulatory network rewiring for secondary metabolism in Arabidopsis thaliana under various conditions
journal, January 2014
- Lv, Qi; Cheng, Rong; Shi, Tieliu
- BMC Plant Biology, Vol. 14, Issue 1
Secondary metabolites in plant innate immunity: conserved function of divergent chemicals
journal, February 2015
- Piasecka, Anna; Jedrzejczak-Rey, Nicolas; Bednarek, Paweł
- New Phytologist, Vol. 206, Issue 3
AraCyc: A Biochemical Pathway Database for Arabidopsis
journal, June 2003
- Mueller, Lukas A.; Zhang, Peifen; Rhee, Seung Y.
- Plant Physiology, Vol. 132, Issue 2
Pathway Correlation Profile of Gene-Gene Co-Expression for Identifying Pathway Perturbation
journal, December 2012
- Tegge, Allison N.; Caldwell, Charles W.; Xu, Dong
- PLoS ONE, Vol. 7, Issue 12
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
journal, September 2005
- Subramanian, A.; Tamayo, P.; Mootha, V. K.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 43, p. 15545-15550
Biotic stress globally downregulates photosynthesis genes: Biotic stress downregulates photosynthesis
journal, September 2010
- Bilgin, Damla D.; Zavala, Jorge A.; Zhu, Jin
- Plant, Cell & Environment, Vol. 33, Issue 10
Photosynthetic light reactions – An adjustable hub in basic production and plant immunity signaling
journal, August 2014
- Kangasjärvi, Saijaliisa; Tikkanen, Mikko; Durian, Guido
- Plant Physiology and Biochemistry, Vol. 81
Glutathione as a signaling molecule - another challenge to pathogens: Another challenge to pathogens
journal, June 2011
- Ghanta, Srijani; Chattopadhyay, Sharmila
- Plant Signaling & Behavior, Vol. 6, Issue 6
Unbalanced Activation of Glutathione Metabolic Pathways Suggests Potential Involvement in Plant Defense against the Gall Midge Mayetiola destructor in Wheat
journal, January 2015
- Liu, Xuming; Zhang, Shize; Whitworth, R. Jeff
- Scientific Reports, Vol. 5, Issue 1
Reactive oxygen species generation and signaling in plants
journal, December 2012
- Tripathy, Baishnab Charan; Oelmüller, Ralf
- Plant Signaling & Behavior, Vol. 7, Issue 12
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
journal, January 1995
- Benjamini, Yoav; Hochberg, Yosef
- Journal of the Royal Statistical Society: Series B (Methodological), Vol. 57, Issue 1
Link-based quantitative methods to identify differentially coexpressed genes and gene Pairs
journal, January 2011
- Yu, Hui; Liu, Bao-Hong; Ye, Zhi-Qiang
- BMC Bioinformatics, Vol. 12, Issue 1
BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks
journal, June 2005
- Maere, S.; Heymans, K.; Kuiper, M.
- Bioinformatics, Vol. 21, Issue 16
DiffCorr: An R package to analyze and visualize differential correlations in biological networks
journal, April 2013
- Fukushima, Atsushi
- Gene, Vol. 518, Issue 1
Crosstalk between abiotic and biotic stress responses: a current view from the points of convergence in the stress signaling networks
journal, August 2006
- Fujita, Miki; Fujita, Yasunari; Noutoshi, Yoshiteru
- Current Opinion in Plant Biology, Vol. 9, Issue 4
Comparing signaling mechanisms engaged in pattern-triggered and effector-triggered immunity
journal, August 2010
- Tsuda, Kenichi; Katagiri, Fumiaki
- Current Opinion in Plant Biology, Vol. 13, Issue 4
Photosynthetic light reactions – An adjustable hub in basic production and plant immunity signaling
journal, August 2014
- Kangasjärvi, Saijaliisa; Tikkanen, Mikko; Durian, Guido
- Plant Physiology and Biochemistry, Vol. 81
From ‘differential expression’ to ‘differential networking’ – identification of dysfunctional regulatory networks in diseases
journal, July 2010
- de la Fuente, Alberto
- Trends in Genetics, Vol. 26, Issue 7
Phytoalexins in defense against pathogens
journal, February 2012
- Ahuja, Ishita; Kissen, Ralph; Bones, Atle M.
- Trends in Plant Science, Vol. 17, Issue 2
Chloroplasts play a central role in plant defence and are targeted by pathogen effectors
journal, June 2015
- de Torres Zabala, Marta; Littlejohn, George; Jayaraman, Siddharth
- Nature Plants, Vol. 1, Issue 6
Unbalanced Activation of Glutathione Metabolic Pathways Suggests Potential Involvement in Plant Defense against the Gall Midge Mayetiola destructor in Wheat
journal, January 2015
- Liu, Xuming; Zhang, Shize; Whitworth, R. Jeff
- Scientific Reports, Vol. 5, Issue 1
Functional Analysis and Characterization of Differential Coexpression Networks
journal, August 2015
- Hsu, Chia-Lang; Juan, Hsueh-Fen; Huang, Hsuan-Cheng
- Scientific Reports, Vol. 5, Issue 1
Network-Based Comparative Analysis of Arabidopsis Immune Responses to Golovinomyces orontii and Botrytis cinerea Infections
journal, January 2016
- Jiang, Zhenhong; Dong, Xiaobao; Zhang, Ziding
- Scientific Reports, Vol. 6, Issue 1
Identification of a novel gene HYS1/CPR5 that has a repressive role in the induction of leaf senescence and pathogen-defence responses in Arabidopsis thaliana
journal, February 2002
- Yoshida, Satoko; Ito, Masaki; Nishida, Ikuo
- The Plant Journal, Vol. 29, Issue 4
Application of
a priori
established gene sets to discover biologically important differential expression in microarray data
journal, October 2005
- Bild, Andrea; Febbo, Phillip George
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 43
Differential coexpression analysis using microarray data and its application to human cancer
journal, October 2005
- Choi, J. K.; Yu, U.; Yoo, O. J.
- Bioinformatics, Vol. 21, Issue 24
Discerning static and causal interactions in genome-wide reverse engineering problems
journal, May 2008
- Zampieri, Mattia; Soranzo, Nicola; Altafini, Claudio
- Bioinformatics, Vol. 24, Issue 13
Photosynthesis, photorespiration, and light signalling in defence responses
journal, January 2012
- Kangasjarvi, S.; Neukermans, J.; Li, S.
- Journal of Experimental Botany, Vol. 63, Issue 4
An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors
journal, March 2015
- Jin, Jinpu; He, Kun; Tang, Xing
- Molecular Biology and Evolution, Vol. 32, Issue 7
The Gene Ontology (GO) database and informatics resource
journal, January 2004
- Gene Ontology Consortium,
- Nucleic Acids Research, Vol. 32, Issue 90001
AGRIS: the Arabidopsis Gene Regulatory Information Server, an update
journal, November 2010
- Yilmaz, A.; Mejia-Guerra, M. K.; Kurz, K.
- Nucleic Acids Research, Vol. 39, Issue Database
Primary Metabolism and Plant Defense—Fuel for the Fire
journal, May 2009
- Bolton, Melvin D.
- Molecular Plant-Microbe Interactions, Vol. 22, Issue 5
AraCyc: A Biochemical Pathway Database for Arabidopsis
journal, June 2003
- Mueller, Lukas A.; Zhang, Peifen; Rhee, Seung Y.
- Plant Physiology, Vol. 132, Issue 2
Deciphering the Arabidopsis Floral Transition Process by Integrating a Protein-Protein Interaction Network and Gene Expression Data
journal, June 2010
- He, Fei; Zhou, Yuan; Zhang, Ziding
- Plant Physiology, Vol. 153, Issue 4
Exploring Tomato Gene Functions Based on Coexpression Modules Using Graph Clustering and Differential Coexpression Approaches
journal, February 2012
- Fukushima, Atsushi; Nishizawa, Tomoko; Hayakumo, Mariko
- Plant Physiology, Vol. 158, Issue 4
Transcriptome and Metabolite Profiling of the Infection Cycle of Zymoseptoria tritici on Wheat Reveals a Biphasic Interaction with Plant Immunity Involving Differential Pathogen Chromosomal Contributions and a Variation on the Hemibiotrophic Lifestyle Definition
journal, January 2015
- Rudd, Jason J.; Kanyuka, Kostya; Hassani-Pak, Keywan
- Plant Physiology, Vol. 167, Issue 3
The U-Box Protein CMPG1 Is Required for Efficient Activation of Defense Mechanisms Triggered by Multiple Resistance Genes in Tobacco and Tomato
journal, March 2006
- González-Lamothe, Rocío; Tsitsigiannis, Dimitrios I.; Ludwig, Andrea A.
- The Plant Cell, Vol. 18, Issue 4
Arabidopsis Defense against Botrytis cinerea : Chronology and Regulation Deciphered by High-Resolution Temporal Transcriptomic Analysis
journal, September 2012
- Windram, Oliver; Madhou, Priyadharshini; McHattie, Stuart
- The Plant Cell, Vol. 24, Issue 9
Transcriptional Dynamics Driving MAMP-Triggered Immunity and Pathogen Effector-Mediated Immunosuppression in Arabidopsis Leaves Following Infection with Pseudomonas syringae pv tomato DC3000
journal, November 2015
- Lewis, Laura A.; Polanski, Krzysztof; de Torres-Zabala, Marta
- The Plant Cell, Vol. 27, Issue 11
Transcriptional networks in plant immunity
journal, January 2015
- Tsuda, Kenichi; Somssich, Imre E.
- New Phytologist, Vol. 206, Issue 3
Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis
journal, June 2016
- He, Fei; Yoo, Shinjae; Wang, Daifeng
- The Plant Journal, Vol. 86, Issue 6
Network Modeling to Understand Plant Immunity
journal, August 2014
- Windram, Oliver; Penfold, Christopher A.; Denby, Katherine J.
- Annual Review of Phytopathology, Vol. 52, Issue 1
DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules
journal, January 2010
- Tesson, Bruno M.; Breitling, Rainer; Jansen, Ritsert C.
- BMC Bioinformatics, Vol. 11, Issue 1
Link-based quantitative methods to identify differentially coexpressed genes and gene Pairs
journal, January 2011
- Yu, Hui; Liu, Bao-Hong; Ye, Zhi-Qiang
- BMC Bioinformatics, Vol. 12, Issue 1
Expression-based network biology identifies immune-related functional modules involved in plant defense
journal, January 2014
- Tully, Joel P.; Hill, Aubrey E.; Ahmed, Hadia MR
- BMC Genomics, Vol. 15, Issue 1
Regulatory network rewiring for secondary metabolism in Arabidopsis thaliana under various conditions
journal, January 2014
- Lv, Qi; Cheng, Rong; Shi, Tieliu
- BMC Plant Biology, Vol. 14, Issue 1
The Arabidopsis Thaliana-Pseudomonas Syringae Interaction
journal, January 2002
- Katagiri, Fumiaki; Thilmony, Roger; He, Sheng Yang
- The Arabidopsis Book, Vol. 1
A Differential Wiring Analysis of Expression Data Correctly Identifies the Gene Containing the Causal Mutation
journal, May 2009
- Hudson, Nicholas J.; Reverter, Antonio; Dalrymple, Brian P.
- PLoS Computational Biology, Vol. 5, Issue 5
Dissection of Regulatory Networks that Are Altered in Disease via Differential Co-expression
journal, March 2013
- Amar, David; Safer, Hershel; Shamir, Ron
- PLoS Computational Biology, Vol. 9, Issue 3
Extensive Decoupling of Metabolic Genes in Cancer
journal, May 2015
- Reznik, Ed; Sander, Chris
- PLOS Computational Biology, Vol. 11, Issue 5
Pathway Correlation Profile of Gene-Gene Co-Expression for Identifying Pathway Perturbation
journal, December 2012
- Tegge, Allison N.; Caldwell, Charles W.; Xu, Dong
- PLoS ONE, Vol. 7, Issue 12
Molecular Signatures in Arabidopsis thaliana in Response to Insect Attack and Bacterial Infection
journal, March 2013
- Barah, Pankaj; Winge, Per; Kusnierczyk, Anna
- PLoS ONE, Vol. 8, Issue 3
DCGL v2.0: An R Package for Unveiling Differential Regulation from Differential Co-expression
journal, November 2013
- Yang, Jing; Yu, Hui; Liu, Bao-Hong
- PLoS ONE, Vol. 8, Issue 11
Discovery of Core Biotic Stress Responsive Genes in Arabidopsis by Weighted Gene Co-Expression Network Analysis
journal, March 2015
- Amrine, Katherine C. H.; Blanco-Ulate, Barbara; Cantu, Dario
- PLOS ONE, Vol. 10, Issue 3
The role of MYB34, MYB51 and MYB122 in the regulation of camalexin biosynthesis in Arabidopsis thaliana
journal, August 2015
- Frerigmann, Henning; Glawischnig, Erich; Gigolashvili, Tamara
- Frontiers in Plant Science, Vol. 6
Large-Scale Public Transcriptomic Data Mining Reveals a Tight Connection between the Transport of Nitrogen and Other Transport Processes in Arabidopsis
journal, August 2016
- He, Fei; Karve, Abhijit A.; Maslov, Sergei
- Frontiers in Plant Science, Vol. 7
Construction and comparison of gene co-expression networks shows complex plant immune responses
journal, January 2014
- Leal, Luis Guillermo; López, Camilo; López-Kleine, Liliana
- PeerJ, Vol. 2
Works referencing / citing this record:
Recent advances in gene function prediction using context-specific coexpression networks in plants
journal, January 2019
- Gupta, Chirag; Pereira, Andy
- F1000Research, Vol. 8
Metric learning on expression data for gene function prediction
journal, September 2019
- Makrodimitris, Stavros; Reinders, Marcel J. T.; van Ham, Roeland C. H. J.
- Bioinformatics
PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System
journal, August 2018
- Qi, Huan; Jiang, Zhenhong; Zhang, Kang
- Genomics, Proteomics & Bioinformatics, Vol. 16, Issue 4
Global temporal dynamic landscape of pathogen-mediated subversion of Arabidopsis innate immunity
journal, August 2017
- Mishra, Bharat; Sun, Yali; Ahmed, Hadia
- Scientific Reports, Vol. 7, Issue 1
Recent advances in gene function prediction using context-specific coexpression networks in plants
journal, January 2019
- Gupta, Chirag; Pereira, Andy
- F1000Research, Vol. 8