Functional characterization of drought-responsive modules and genes in Oryza sativa: a network-based approach

Annotation of gene function in citrus using gene expression information and co-expression networks

(2014) Darren CJ Wong et al.   BMC PLANT BIOLOGY

AraNet v2: an improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species

(2014) Tak Lee et al.   NUCLEIC ACIDS RESEARCH

Roles of Gibberellin Catabolism and Signaling in Growth and Physiological Response to Drought and Short-Day Photoperiods in Populus Trees

(2014) Christine Zawaski et al.   PLoS One

Transcriptional responses of Arabidopsis thaliana to chewing and sucking insect herbivores

(2014) Heidi M. Appel et al.   Frontiers in Plant Science

Construction and validation of a gene co-expression network in grapevine (Vitis vinifera. L.)

(2014) Ying-Hai Liang et al.   Horticulture Research

Gramene 2013: comparative plant genomics resources

(2013) Marcela K. Monaco et al.   NUCLEIC ACIDS RESEARCH

TheArabidopsis GIBBERELLIN METHYL TRANSFERASE 1suppresses gibberellin activity, reduces whole-plant transpiration and promotes drought tolerance in transgenic tomato

(2013) IDO NIR et al.   PLANT CELL AND ENVIRONMENT

The roles of two transcription factors, ABI4 and CBFA, in ABA and plastid signalling and stress responses

(2013) Zhong-Wei Zhang et al.   PLANT MOLECULAR BIOLOGY

Genes and Co-Expression Modules Common to Drought and Bacterial Stress Responses in Arabidopsis and Rice

(2013) Rafi Shaik et al.   PLoS One

Auxin controls seed dormancy through stimulation of abscisic acid signaling by inducing ARF-mediated ABI3 activation in Arabidopsis

(2013) X. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Towards revealing the functions of all genes in plants

(2013) Seung Yon Rhee et al.   TRENDS IN PLANT SCIENCE

Abiotic and Biotic Stress Responses in Group Phureja DM1-3 516 R44 as Measured through Whole Transcriptome Sequencing

(2013) Alicia N. Massa et al.   Plant Genome

DeGNServer: Deciphering Genome-Scale Gene Networks through High Performance Reverse Engineering Analysis

(2013) Jun Li et al.   Biomed Research International

MetNet Online: a novel integrated resource for plant systems biology

(2012) Yves Sucaet et al.   BMC BIOINFORMATICS

Cis-regulatory signatures of orthologous stress-associated bZIP transcription factors from rice, sorghum and Arabidopsis based on phylogenetic footprints

(2012) Fuyu Xu et al.   BMC GENOMICS

Adipose Co-expression networks across Finns and Mexicans identify novel triglyceride-associated genes

(2012) Blake E Haas et al.   BMC Medical Genomics

A R2R3-type MYB gene, OsMYB2, is involved in salt, cold, and dehydration tolerance in rice

(2012) An Yang et al.   JOURNAL OF EXPERIMENTAL BOTANY

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

Genome-wide temporal-spatial gene expression profiling of drought responsiveness in rice

(2011) Di Wang et al.   BMC GENOMICS

ABA biosynthesis and degradation contributing to ABA homeostasis during barley seed development under control and terminal drought-stress conditions

(2011) Christiane Seiler et al.   JOURNAL OF EXPERIMENTAL BOTANY

Transcriptomic analysis of autistic brain reveals convergent molecular pathology

(2011) Irina Voineagu et al.   NATURE

Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm

(2011) Xuehui Huang et al.   NATURE GENETICS

An Omics Approach to Understand the Plant Abiotic Stress

(2011) Mousumi Debnath et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species

(2011) M. Mutwil et al.   PLANT CELL

Comparative Network Analysis Reveals That Tissue Specificity and Gene Function Are Important Factors Influencing the Mode of Expression Evolution in Arabidopsis and Rice

(2011) S. Movahedi et al.   PLANT PHYSIOLOGY

Gene Coexpression Network Alignment and Conservation of Gene Modules between Two Grass Species: Maize and Rice

(2011) S. P. Ficklin et al.   PLANT PHYSIOLOGY

Gene Coexpression Network Analysis as a Source of Functional Annotation for Rice Genes

(2011) Kevin L. Childs et al.   PLoS One

Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions

(2011) G. W. Bassel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic dissection of the biotic stress response using a genome-scale gene network for rice

(2011) I. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detecting Novel Associations in Large Data Sets

(2011) D. N. Reshef et al.   SCIENCE

Is My Network Module Preserved and Reproducible?

(2011) Peter Langfelder et al.   PLoS Computational Biology

Auxin Biosynthesis and Its Role in Plant Development

(2010) Yunde Zhao   Annual Review of Plant Biology

Assigning biological functions to rice genes by genome annotation, expression analysis and mutagenesis

(2010) Shu-Ye Jiang et al.   BIOTECHNOLOGY LETTERS

Rice DENSE AND ERECT PANICLE 2 is essential for determining panicle outgrowth and elongation

(2010) Feng Li et al.   CELL RESEARCH

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

Gene Structures, Classification and Expression Models of the AP2/EREBP Transcription Factor Family in Rice

(2010) Akhter Most Sharoni et al.   PLANT AND CELL PHYSIOLOGY

Coexpression Analysis Identifies Rice Starch Regulator1, a Rice AP2/EREBP Family Transcription Factor, as a Novel Rice Starch Biosynthesis Regulator

(2010) F.-F. Fu et al.   PLANT PHYSIOLOGY

Arabidopsis gene co-expression network and its functional modules

(2009) Linyong Mao et al.   BMC BIOINFORMATICS

A new role for plant R2R3-MYB transcription factors in cell cycle regulation

(2009) Eleonora Cominelli et al.   CELL RESEARCH

Transgenic expression of MYB15 confers enhanced sensitivity to abscisic acid and improved drought tolerance in Arabidopsis thaliana

(2009) Zhenhua Ding et al.   Journal of Genetics and Genomics

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

The Arabidopsis ABA-INSENSITIVE (ABI) 4 factor acts as a central transcription activator of the expression of its own gene, and for the induction ofABI5andSBE2.2 genesduring sugar signaling

(2009) Flavia Bossi et al.   PLANT JOURNAL

Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks

(2009) K. Vandepoele et al.   PLANT PHYSIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

A Systems Level Analysis of Transcriptional Changes in Alzheimer's Disease and Normal Aging

(2008) J. A. Miller et al.   JOURNAL OF NEUROSCIENCE

MYB transcription factors that colour our fruit

(2008) Andrew C. Allan et al.   TRENDS IN PLANT SCIENCE