PlantExpress: A Database Integrating OryzaExpress and ArthaExpress for Single-species and Cross-species Gene Expression Network Analyses with Microarray-Based Transcriptome Data

The Plant Genome Integrative Explorer Resource: PlantGenIE.org

(2015) David Sundell et al.   NEW PHYTOLOGIST

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

ALCOdb: Gene Coexpression Database for Microalgae

(2015) Yuichi Aoki et al.   PLANT AND CELL PHYSIOLOGY

TENOR: Database for Comprehensive mRNA-Seq Experiments in Rice

(2015) Yoshihiro Kawahara et al.   PLANT AND CELL PHYSIOLOGY

ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression

(2015) Yuichi Aoki et al.   PLANT AND CELL PHYSIOLOGY

ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa

(2014) Sergiu Netotea et al.   BMC GENOMICS

The transcriptional network of WRKY53 in cereals links oxidative responses to biotic and abiotic stress inputs

(2014) Leon Van Eck et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

AtCAST3.0 Update: A Web-Based Tool for Analysis of Transcriptome Data by Searching Similarities in Gene Expression Profiles

(2014) Yusuke Kakei et al.   PLANT AND CELL PHYSIOLOGY

Plant Omics Data Center: An Integrated Web Repository for Interspecies Gene Expression Networks with NLP-Based Curation

(2014) Hajime Ohyanagi et al.   PLANT AND CELL PHYSIOLOGY

UniVIO: A Multiple Omics Database with Hormonome and Transcriptome Data from Rice

(2013) Toru Kudo et al.   PLANT AND CELL PHYSIOLOGY

Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics

(2013) Hiroaki Sakai et al.   PLANT AND CELL PHYSIOLOGY

RiceXPro Version 3.0: expanding the informatics resource for rice transcriptome

(2012) Yutaka Sato et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

BAR expressolog identification: expression profile similarity ranking of homologous genes in plant species

(2012) Rohan V. Patel et al.   PLANT JOURNAL

AtPUB19, a U-Box E3 Ubiquitin Ligase, Negatively Regulates Abscisic Acid and Drought Responses in Arabidopsis thaliana

(2011) Yong-Chang Liu et al.   Molecular Plant

PLEXdb: gene expression resources for plants and plant pathogens

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

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

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

(2011) M. Mutwil et al.   PLANT CELL

Rice Ethylene-Response AP2/ERF Factor OsEATB Restricts Internode Elongation by Down-Regulating a Gibberellin Biosynthetic Gene

(2011) Weiwei Qi et al.   PLANT PHYSIOLOGY

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

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

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

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Identification of up-regulated genes in flag leaves during rice grain filling and characterization of OsNAC5, a new ABA-dependent transcription factor

(2009) Raul A. Sperotto et al.   PLANTA

Hd3a and RFT1 are essential for flowering in rice

(2008) R. Komiya et al.   DEVELOPMENT