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

Characterizing gene coexpression modules in Oryza sativa based on a graph-clustering approach

(2011) Atsushi Fukushima et al.   Plant Biotechnology

CoP: a database for characterizing co-expressed gene modules with biological information in plants

(2010) Y. Ogata et al.   BIOINFORMATICS

On the Choice and Number of Microarrays for Transcriptional Regulatory Network Inference

(2010) Elissa J Cosgrove et al.   BMC BIOINFORMATICS

Genetic diversity and striatal gene networks: focus on the heterogeneous stock-collaborative cross (HS-CC) mouse

(2010) Ovidiu D Iancu et al.   BMC GENOMICS

Genome-wide gene responses in a transgenic rice line carrying the maize resistance gene Rxo1 to the rice bacterial streak pathogen, Xanthomonas oryzae pv. oryzicola

(2010) Yong-Li Zhou et al.   BMC GENOMICS

Coexpression Network Analysis Identifies Transcriptional Modules Related to Proastrocytic Differentiation and Sprouty Signaling in Glioma

(2010) A. E. Ivliev et al.   CANCER RESEARCH

Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana

(2010) Insuk Lee et al.   NATURE BIOTECHNOLOGY

Detecting network modules in fMRI time series: A weighted network analysis approach

(2010) Jeanette A. Mumford et al.   NEUROIMAGE

OryzaExpress: An Integrated Database of Gene Expression Networks and Omics Annotations in Rice

(2010) Kazuki Hamada et al.   PLANT AND CELL PHYSIOLOGY

ArabidopsisRETINOBLASTOMA-RELATED Is Required for Stem Cell Maintenance, Cell Differentiation, and Lateral Organ Production

(2010) Lorenzo Borghi et al.   PLANT CELL

Tissue-Adapted Invasion Strategies of the Rice Blast FungusMagnaporthe oryzae

(2010) Sylvain Marcel et al.   PLANT CELL

The Association of Multiple Interacting Genes with Specific Phenotypes in Rice Using Gene Coexpression Networks

(2010) Stephen P. Ficklin et al.   PLANT PHYSIOLOGY

Gene Bionetwork Analysis of Ovarian Primordial Follicle Development

(2010) Eric E. Nilsson et al.   PLoS One

Identifying Modules of Coexpressed Transcript Units and Their Organization of Saccharopolyspora erythraea from Time Series Gene Expression Profiles

(2010) Xiao Chang et al.   PLoS One

OsWRKY IIa Transcription Factors Modulate Rice Innate Immunity

(2010) Ying Peng et al.   Rice

Arabidopsis gene co-expression network and its functional modules

(2009) Linyong Mao et al.   BMC BIOINFORMATICS

Gene Expression Atlas at the European Bioinformatics Institute

(2009) Misha Kapushesky et al.   NUCLEIC ACIDS RESEARCH

Highly Sensitive and High-Throughput Analysis of Plant Hormones Using MS-Probe Modification and Liquid Chromatography–Tandem Mass Spectrometry: An Application for Hormone Profiling in Oryza sativa

(2009) Mikiko Kojima et al.   PLANT AND CELL PHYSIOLOGY

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

(2009) BJ��RN USADEL et al.   PLANT CELL AND ENVIRONMENT

A dynamic gene expression atlas covering the entire life cycle of rice

(2009) Lei Wang et al.   PLANT JOURNAL

Assembly of an Interactive Correlation Network for the Arabidopsis Genome Using a Novel Heuristic Clustering Algorithm

(2009) M. Mutwil et al.   PLANT PHYSIOLOGY

Physiological and Transcriptome Analysis of Iron and Phosphorus Interaction in Rice Seedlings

(2009) L. Zheng et al.   PLANT PHYSIOLOGY

RiceArrayNet: A Database for Correlating Gene Expression from Transcriptome Profiling, and Its Application to the Analysis of Coexpressed Genes in Rice

(2009) T.-H. Lee et al.   PLANT PHYSIOLOGY

Defining Core Metabolic and Transcriptomic Responses to Oxygen Availability in Rice Embryos and Young Seedlings

(2009) R. Narsai et al.   PLANT PHYSIOLOGY

arrayQualityMetrics—a bioconductor package for quality assessment of microarray data

(2008) Audrey Kauffmann et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Rice–arsenate interactions in hydroponics: whole genome transcriptional analysis

(2008) Gareth J. Norton et al.   JOURNAL OF EXPERIMENTAL BOTANY

Global patterns of gene expression in rice cultivars undergoing a susceptible or resistant interaction with the parasitic plantStriga hermonthica

(2008) P. J. Swarbrick et al.   NEW PHYTOLOGIST

NCBI GEO: archive for high-throughput functional genomic data

(2008) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

Molecular and genomic basis of volatile-mediated indirect defense against insects in rice

(2008) Joshua S. Yuan et al.   PLANT JOURNAL

Experimental Analysis of the Rice Mitochondrial Proteome, Its Biogenesis, and Heterogeneity

(2008) S. Huang et al.   PLANT PHYSIOLOGY

The Arabidopsis A4 Subfamily of Lectin Receptor Kinases Negatively Regulates Abscisic Acid Response in Seed Germination

(2008) Z. Xin et al.   PLANT PHYSIOLOGY

Expansion and Diversification of the Populus R2R3-MYB Family of Transcription Factors

(2008) O. Wilkins et al.   PLANT PHYSIOLOGY