RiceFREND: a platform for retrieving coexpressed gene networks in rice

Inflorescence Meristem Identity in Rice Is Specified by Overlapping Functions of Three AP1/FUL-Like MADS Box Genes and PAP2, a SEPALLATA MADS Box Gene

(2012) K. Kobayashi et al.   PLANT CELL

Field transcriptome revealed critical developmental and physiological transitions involved in the expression of growth potential in japonica rice

(2011) Yutaka Sato et al.   BMC PLANT BIOLOGY

PLEXdb: gene expression resources for plants and plant pathogens

(2011) S. Dash et al.   NUCLEIC ACIDS RESEARCH

ATTED-II Updates: Condition-Specific Gene Coexpression to Extend Coexpression Analyses and Applications to a Broad Range of Flowering Plants

(2011) T. Obayashi et al.   PLANT AND CELL PHYSIOLOGY

Genome-wide transcriptome dissection of the rice root system: implications for developmental and physiological functions

(2011) Hinako Takehisa et al.   PLANT JOURNAL

Cytoscape Web: an interactive web-based network browser

(2010) Christian T. Lopes et al.   BIOINFORMATICS

Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways

(2010) Takeshi Obayashi et al.   JOURNAL OF PLANT RESEARCH

PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database

(2010) He Zhang et al.   NUCLEIC ACIDS RESEARCH

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments

(2010) H. Parkinson et al.   NUCLEIC ACIDS RESEARCH

RiceXPro: a platform for monitoring gene expression in japonica rice grown under natural field conditions

(2010) Y. Sato et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

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

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

Rank of Correlation Coefficient as a Comparable Measure for Biological Significance of Gene Coexpression

(2009) T. Obayashi et al.   DNA RESEARCH

A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies

(2009) Yuling Jiao et al.   NATURE GENETICS

SALAD database: a motif-based database of protein annotations for plant comparative genomics

(2009) Motohiro Mihara et al.   NUCLEIC ACIDS RESEARCH

PlnTFDB: updated content and new features of the plant transcription factor database

(2009) Paulino Pérez-Rodríguez et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Lei Wang et al.   PLANT JOURNAL

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

GeneCAT—novel webtools that combine BLAST and co-expression analyses

(2008) Marek Mutwil et al.   NUCLEIC ACIDS RESEARCH

KEGG Atlas mapping for global analysis of metabolic pathways

(2008) S. Okuda et al.   NUCLEIC ACIDS RESEARCH

ATTED-II provides coexpressed gene networks for Arabidopsis

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

Genome-wide targeted prediction of ABA responsive genes in rice based on over-represented cis-motif in co-expressed genes

(2008) Sangram K. Lenka et al.   PLANT MOLECULAR BIOLOGY

CressExpress: A Tool For Large-Scale Mining of Expression Data from Arabidopsis

(2008) V. Srinivasasainagendra et al.   PLANT PHYSIOLOGY