We use cookies to enhance your experience on our website. By continuing to use our website, you are agreeing to our use of cookies. You can change your cookie settings at any time. Find out more Skip to Main Content

DATABASE ARTICLES

PCP publishes an annual collection of articles describing new or updated databases and free online reference tools of broad and specialist interest to plant scientists; this is a great opportunity to share your knowledge within the research community! 

We are now accepting pre-submission inquiries for the 2018 Database Issue. Authors interested in submitting a database manuscript should contact the editorial office with an abstract and URL of the database or online tool, together with a completed online pre-submission form, which can be downloaded here. The deadline for pre-submission inquiries is no later than 1st July 2017. If approved, authors will be invited to submit their manuscripts no later than 1st September 2017

For more information, please refer to our online instructions or contact the editorial office (email to:pcp.editorialoffice@oup.com). 



A LIST OF PUBLISHED DATABASE ARTICLES:

PlantExpress: A Database Integrating OryzaExpress and ArthaExpress for Single-species and Cross-species Gene Expression Network Analyses with Microarray-Based Transcriptome Data
Toru Kudo, et al.
Plant Cell Physiol (2017) 58 (1): e1. DOI: 10.1093/pcp/pcw208

PlantRGDB: A Database of Plant Retrocopied Genes 
Yi Wang
Plant Cell Physiol (2017) 58 (1): e2. DOI: 10.1093/pcp/pcw210

CATchUP: A Web Database for Spatiotemporally Regulated Genes 
Yukino Nakamura, et al.
Plant Cell Physiol (2017) 58 (1): e3. DOI: 10.1093/pcp/pcw199

ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery 
Vivek Krishnakumar, et al.
Plant Cell Physiol (2017) 58 (1): e4. DOI: 10.1093/pcp/pcw200

MarpoDB: An Open Registry for Marchantia Polymorpha Genetic Parts 
Mihails Delmans, et al.
Plant Cell Physiol (2017) 58 (1): e5. DOI: 10.1093/pcp/pcw201

Alga-PrAS (Algal Protein Annotation Suite): A Database of Comprehensive Annotation in Algal Proteomes 
Atsushi Kurotani, et al.
Plant Cell Physiol (2017) 58 (1): e6. DOI: 10.1093/pcp/pcw212

Enhancing the GABI-Kat Arabidopsis thaliana T-DNA Insertion Mutant Database by Incorporating Araport11 Annotation 
Nils Kleinboelting, et al.
Plant Cell Physiol (2017) 58 (1): e7. DOI: 10.1093/pcp/pcw205

TOMATOMICS: A Web Database for Integrated Omics Information in Tomato 
Toru Kudo, et al.
Plant Cell Physiol (2017) 58 (1): e8. DOI: 10.1093/pcp/pcw207

Orchidstra 2.0—A Transcriptomics Resource for the Orchid Family 
Ya-Ting Chao, et al.
Plant Cell Physiol (2017) 58 (1): e9. DOI: 10.1093/pcp/pcw220

PCoM-DB Update: A Protein Co-Migration Database for Photosynthetic Organisms 
Atsushi Takabayashi, et al.
Plant Cell Physiol (2017) 58 (1): e10. DOI: 10.1093/pcp/pcw219

OryzaGenome: Genome Diversity Database of Wild Oryza Species
Hajime Ohyanagi, et al. 
Plant Cell Physiol (2016) 57 (1): e1. doi: 10.1093/pcp/pcv171

The Vigna Genome Server, ‘VigGS’ : A Genomic Knowledge Base of the Genus Vigna Based on High-Quality, Annotated Genome Sequence of the Azuki Bean, Vigna angularis (Willd.) Ohwi & Ohashi 
Hiroaki Sakai, et al. 
Plant Cell Physiol (2016) 57 (1): e2 doi:10.1093/pcp/pcv189

ALCOdb: Gene Coexpression Database for Microalgae
Yuichi Aoki, et al. 
Plant Cell Physiol (2016) 57 (1): e3 doi:10.1093/pcp/pcv190

Boosting AthaMap Database Content with Data from Protein Binding Microarrays
Reinhard Hehl, et al. 
Plant Cell Physiol (2016) 57 (1): e4 doi:10.1093/pcp/pcv156

ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression
Yuichi Aoki, et al. 
Plant Cell Physiol (2016) 57 (1): e5 doi:10.1093/pcp/pcv165

Pleurochrysome: A Web Database of Pleurochrysis Transcripts and Orthologs Among Heterogeneous Algae
Naoki Yamamoto, et al. 
Plant Cell Physiol (2016) 57 (1): e6 doi:10.1093/pcp/pcv195

TENOR: Database for Comprehensive mRNA-Seq Experiments in Rice
Yoshihiro Kawahara, et al. 
Plant Cell Physiol (2016) 57 (1): e7 doi:10.1093/pcp/pcv179

CANTATAdb: A Collection of Plant Long Non-Coding RNAs
Michał W. Szcześniak, et al. 
Plant Cell Physiol (2016) 57 (1): e8 doi:10.1093/pcp/pcv201

Editor's Choice: Finding the Subcellular Location of Barley, Wheat, Rice and Maize Proteins: The Compendium of Crop Proteins with Annotated Locations (cropPAL)
Cornelia M. Hooper, et al. 
Plant Cell Physiol (2016) 57 (1): e9 doi:10.1093/pcp/pcv170

eHALOPH a Database of Salt-Tolerant Plants: Helping put Halophytes to Work
Joaquim Santos, et al. 
Plant Cell Physiol (2016) 57 (1): e10 doi:10.1093/pcp/pcv155

TOMATOMA Update: Phenotypic and Metabolite Information in the Micro-Tom Mutant Resource
Masahito Shikata, et al. 
Plant Cell Physiol (2016) 57 (1): e11 doi:10.1093/pcp/pcv194

HRGRN: A Graph Search-Empowered Integrative Database of Arabidopsis Signaling Transduction, Metabolism and Gene Regulation Networks
Xinbin Dai, et al. 
Plant Cell Physiol (2016) 57 (1): e12 doi:10.1093/pcp/pcv200

MTGD: The Medicago truncatula Genome Database
Vivek Krishnakumar, et al. 
Plant Cell Physiol (2015) 56 (1): e1. doi: 10.1093/pcp/pcu179

Sinbase: An Integrated Database to Study Genomics, Genetics and Comparative Genomics inSesamum indicum
Linhai Wang, et al. 
Plant Cell Physiol (2015) 56 (1): e2 doi:10.1093/pcp/pcu175

Triticeae Resources in Ensembl Plants
Dan M. Bolser, et al. 
Plant Cell Physiol (2015) 56 (1): e3 doi:10.1093/pcp/pcu183

GenomicusPlants: A Web Resource to Study Genome Evolution in Flowering Plants
Alexandra Louis, et al. 
Plant Cell Physiol (2015) 56 (1): e4 doi:10.1093/pcp/pcu177

De Novo Transcriptome Assembly of a Fern, Lygodium japonicum , and a Web Resource Database, Ljtrans DB
Koichiro Aya, et al. 
Plant Cell Physiol (2015) 56 (1): e5 doi:10.1093/pcp/pcu184

MOROKOSHI: Transcriptome Database in Sorghum bicolor
Yuko Makita, et al. 
Plant Cell Physiol (2015) 56 (1): e6 doi:10.1093/pcp/pcu187

AtCAST3.0 Update: A Web-Based Tool for Analysis of Transcriptome Data by Searching Similarities in Gene Expression Profiles
Yusuke Kakei and Yukihisa Shimada 
Plant Cell Physiol (2015) 56 (1): e7 doi:10.1093/pcp/pcu174

LAILAPS: The Plant Science Search Engine
Maria Esch, et al. 
Plant Cell Physiol (2015) 56 (1): e8 doi:10.1093/pcp/pcu185

Plant Omics Data Center: An Integrated Web Repository for Interspecies Gene Expression Networks with NLP-Based Curation
Hajime Ohyanagi, et al. 
Plant Cell Physiol (2015) 56 (1): e9 doi:10.1093/pcp/pcu188

MPIC: A Mitochondrial Protein Import Components Database for Plant and Non-Plant Species
Monika W. Murcha, et al. 
Plant Cell Physiol (2015) 56 (1): e10 doi:10.1093/pcp/pcu186

Plant-PrAS: A Database of Physicochemical and Structural Properties and Novel Functional Regions in Plant Proteomes
Atsushi Kurotani, et al. 
Plant Cell Physiol (2015) 56 (1): e11 doi:10.1093/pcp/pcu176

A Maize Database Resource that Captures Tissue-Specific and Subcellular-Localized Gene Expression, via Fluorescent Tags and Confocal Imaging (Maize Cell Genomics Database)
Vivek Krishnakumar, et al. 
Plant Cell Physiol (2015) 56 (1): e12 doi:10.1093/pcp/pcu178

The Plant Organelles Database 3 (PODB3) Update 2014: Integrating Electron Micrographs and New Options for Plant Organelle Research
Shoji Mano, et al. 
Plant Cell Physiol (2014) 55(1) doi:10.1093/pcp/pct140 First published online: October 3, 2013 

MEGANTE: A Web-Based System for Integrated Plant Genome Annotation
Hisataka Numa and Takeshi Itoh 
Plant Cell Physiol (2014) 55(1) doi:10.1093/pcp/pct157 First published online: November 18, 2013 

BrassiBase: Introduction to a Novel Knowledge Database on Brassicaceae Evolution
Markus Kiefer, et al. 
Plant Cell Physiol (2014) 55(1) doi:10.1093/pcp/pct158 First published online: November 19, 2013

RARGE II: An Integrated Phenotype Database of Arabidopsis Mutant Traits Using a Controlled Vocabulary
Kenji Akiyama, et al. 
Plant Cell Physiol (2014) 55(1) doi:10.1093/pcp/pct165 First published online: November 21, 2013 

SABRE2: A Database Connecting Plant EST/Full-Length cDNA Clones with Arabidopsis Information
Kaoru Fukami-Kobayashi, et al. 
Plant Cell Physiol (2014) 55(1) doi:10.1093/pcp/pct177 First published online: December 9, 2013 

ATTED-II in 2014: Evaluation of Gene Coexpression in Agriculturally Important Plants
 
Takeshi Obayashi, et al. 
Plant Cell Physiol (2014) 55(1) doi:10.1093/pcp/pct178 First published online: December 10, 2013

KNApSAcK Metabolite Activity Database for Retrieving the Relationships Between Metabolites and Biological Activities
Yukiko Nakamura, et al. 
Plant Cell Physiol (2014) 55(1) doi:10.1093/pcp/pct176 First published online: November 27, 2013 

Plant Genome DataBase Japan (PGDBj): A Portal Website for the Integration of Plant Genome-Related Databases
Erika Asamizu, et al. 
Plant Cell Physiol (2014) 55(1) doi:10.1093/pcp/pct189 First published online: December 19, 2013 

HapRice, an SNP Haplotype Database and a Web Tool for Rice
Jun-ichi Yonemaru, Kaworu Ebana, and Masahiro Yano 
Plant Cell Physiol (2014) 55(1) doi:10.1093/pcp/pct188 First published online: December 13, 2013

CathaCyc, a metabolic pathway database built from Catharanthus roseus RNA-Seq data
Alex Van Moerkercke, et al. 
Plant Cell Physiol (2013) 54(5) doi:10.1093/pcp/pct039 First published online: March 14, 2013

The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses
Laurel Cooper, et al. 
Plant Cell Physiol (2013) 54(2): e1 doi:10.1093/pcp/pcs163 First published online: December 5, 2012 

The Chloroplast Function Database II: A Comprehensive Collection of Homozygous Mutants and Their Phenotypic/Genotypic Traits for Nuclear-Encoded Chloroplast Proteins
Fumiyoshi Myouga, et al. 
Plant Cell Physiol (2013) 54 (2): e2. doi: 10.1093/pcp/pcs171 First published online: December 10, 2012

RadishBase: A Database for Genomics and Genetics of Radish
Di Shen, et al. 
Plant Cell Physiol (2013) 54(2): e3 doi:10.1093/pcp/pcs176 First published online: December 13, 2012 

KNApSAcK-3D: A Three-Dimensional Structure Database of Plant Metabolites
 
Kensuke Nakamura, et al. 
Plant Cell Physiol (2013) 54(2): e4 doi:10.1093/pcp/pcs186 First published online: January 3, 2013 

PRIMe Update: Innovative Content for Plant Metabolomics and Integration of Gene Expression and Metabolite Accumulation
Tetsuya Sakurai, et al. 
Plant Cell Physiol (2013) 54(2): e5 doi:10.1093/pcp/pcs184 First published online: January 3, 2013

Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics
Hiroaki Sakai, et al. 
Plant Cell Physiol (2013) 54(2): e6 doi:10.1093/pcp/pcs183 First published online: December 7, 2013 

OrchidBase 2.0: Comprehensive Collection of Orchidaceae Floral Transcriptomes
Wen-Chieh Tsai, et al. 
Plant Cell Physiol (2013) 54(2): e7 doi:10.1093/pcp/pcs187 First published online: January 10, 2013

STIFDB2: An Updated Version of Plant Stress-Responsive TranscrIption Factor DataBase with Additional Stress Signals, Stress-Responsive Transcription Factor Binding Sites and Stress-Responsive Genes in Arabidopsis and Rice
Mahantesha Naika, et al. 
Plant Cell Physiol (2013) 54(2): e8 doi:10.1093/pcp/pcs185 First published online: January 10, 2013 

UniVIO: A Multiple Omics Database with Hormonome and Transcriptome Data from Rice
Toru Kudo, et al. 
Plant Cell Physiol (2013) 54(2): e9 doi:10.1093/pcp/pct003 First published online: January 10, 2013 

ERISdb: A Database of Plant Splice Sites and Splicing Signals
Michał Wojciech Szcześniak, et al. 
Plant Cell Physiol (2013) 54(2): e10 doi:10.1093/pcp/pct001 First published online: January 7, 2013

Orchidstra: An Integrated Orchid Functional Genomics Database
Chun-lin Su, et al. 
Plant Cell Physiol (2013) 54(2): e11 doi:10.1093/pcp/pct004 First published online: January 16, 2013

WheatGenome.info: An Integrated Database and Portal for Wheat Genome Information
Kaitao Lai, et al. 
Plant Cell Physiol. (2012) 53(2): e2 doi:10.1093/pcp/pcr141 First published online: October 18, 2011

KNApSAcK Family Databases: Integrated Metabolite–Plant Species Databases for Multifaceted Plant Research
Farit Mochamad Afendi, et al. 
Plant Cell Physiol. (2012) 53(2): e1 doi:10.1093/pcp/pcr165 First published online: November 28, 2011

RiceFOX: A Database of Arabidopsis Mutant Lines Overexpressing Rice Full-Length cDNA that Contains a Wide Range of Trait Information to Facilitate Analysis of Gene Function
Tetsuya Sakurai, et al. 
Plant Cell Physiol. (2011) 52(2): 265-273 first published online December 23, 2010 doi:10.1093/pcp/pcq190

ARTADE2DB: Improved Statistical Inferences for Arabidopsis Gene Functions and Structure Predictions by Dynamic Structure-Based Dynamic Expression (DSDE) Analyses
Kei Iida, et al. 
Plant Cell Physiol. (2011) 52(2): 254-264 first published online January 12, 2011 doi:10.1093/pcp/pcq202

The Plant Organelles Database 2 (PODB2): An Updated Resource Containing Movie Data of Plant Organelle Dynamics
Shoji Mano, et al. 
Plant Cell Physiol. (2011) 52(2): 244-253 first published online November 28, 2010 doi:10.1093/pcp/pcq184 

Editor's Choice: OrchidBase: A Collection of Sequences of the Transcriptome Derived from Orchids
Chih-Hsiung Fu, et al. 
Plant Cell Physiol. (2011) 52(2): 23238-243 first published online January 17, 2011 doi:10.1093/pcp/pcq201

Rice TOGO Browser: A Platform to Retrieve Integrated Information on Rice Functional and Applied Genomics
Yoshiaki Nagamura, et al. 
Plant Cell Physiol. (2011) 52(2): 230-237 first published online January 6, 2011 doi:10.1093/pcp/pcq197

OryzaExpress: An Integrated Database of Gene Expression Networks and Omics Annotations in Rice
Kazuki Hamada, et al. 
Plant Cell Physiol. (2011) 52(2): 220-229 first published online December 23, 2010 doi:10.1093/pcp/pcq195

ATTED-II Updates: Condition-Specific Gene Coexpression to Extend Coexpression Analyses and Applications to a Broad Range of Flowering Plants
Takeshi Obayashi, et al. 
Plant Cell Physiol. (2011) 52(2): 213-219 first published online January 7, 2011 doi:10.1093/pcp/pcq203

Advances in Omics and Bioinformatics Tools for Systems Analyses of Plant Functions
Keiichi Mochida and Kazuo Shinozaki 
Plant Cell Physiol (2011) 52(12): 2017-2038 doi:10.1093/pcp/pcr153 

Tomato TILLING Technology: Development of a Reverse Genetics Tool for the Efficient Isolation of Mutants from Micro-Tom Mutant Libraries
Yoshihiro Okabe, et al. 
Plant Cell Physiol (2011) 52(11): 1994-2005 first published online September 30, 2011 doi:10.1093/pcp/pcr134

TOMATOMA: A Novel Tomato Mutant Database Distributing Micro-Tom Mutant Collections
Takeshi Saito, et al. 
Plant Cell Physiol (2011) 52(2): 283-296 first published online January 21, 2011 doi:10.1093/pcp/pcr004 

AtCAST, a Tool for Exploring Gene Expression Similarities among DNA Microarray Experiments Using Networks
Eriko Sasaki, et al. 
Plant Cell Physiol (2011) 52(1): 169-180 first published online November 26, 2010 doi:10.1093/pcp/pcq185

Genomics and Bioinformatics Resources for Crop Improvement
Keiichi Mochida and Kazuo Shinozaki 
Plant Cell Physiol (2010) 51(4): 497-523 first published online March 5, 2010 doi:10.1093/pcp/pcq027 

RESOPS: A Database for Analyzing the Correspondence of RNA Editing Sites to Protein Three-Dimensional Structures 
Kei Yura, et al. 
Plant Cell Physiol (2009) 50(11): 1865-1873 first published online October 6, 2009 doi:10.1093/pcp/pcp132

PosMed-plus: An Intelligent Search Engine that Inferentially Integrates Cross-Species Information Resources for Molecular Breeding of Plants
Yuko Makita, et al. 
Plant Cell Physiol (2009) 50(7): 1249-1259 first published online June 15, 2009 doi:10.1093/pcp/pcp086

Omics and Bioinformatics: An Essential Toolbox for Systems Analyses of Plant Functions Beyond 2010
Kazuo Shinozaki and Hitoshi Sakakibara 
Plant Cell Physiol (2009) 50(7): 1177-1180 doi:10.1093/pcp/pcp085 

KAGIANA: An Excel-Based Tool for Retrieving Summary Information on Arabidopsis Genes
Yoshiyuki Ogata, et al. 
Plant Cell Physiol (2009) 50(1): 173-177 first published online November 28, 2008 doi:10.1093/pcp/pcn179

Approaches for Extracting Practical Information from Gene Co-expression Networks in Plant Biology
Koh Aoki, Yoshiyuki Ogata, and Daisuke Shibata 
Plant Cell Physiol (2007) 48(3): 381-390 first published online January 23, 2007 doi:10.1093/pcp/pcm013 

plprot: A Comprehensive Proteome Database for Different Plastid Types
Torsten Kleffmann, et al. 
Plant Cell Physiol (March 2006) 47(3): 432-436 first published online January 17, 2006 doi:10.1093/pcp/pcj005

Biological Ontologies in Rice Databases. An Introduction to the Activities in Gramene and Oryzabase
Yukiko Yamazaki and Pankaj Jaiswal 
Plant Cell Physiol (2005) 46(1): 63-68 first published online January 19, 2005 doi:10.1093/pcp/pci505 

From Mapping to Sequencing, Post-sequencing and Beyond
Takuji Sasaki, et al. 
Plant Cell Physiol (2005) 46(1): 3-13 first published online January 19, 2005 doi:10.1093/pcp/pci503

This Feature Is Available To Subscribers Only

Sign In or Create an Account

This PDF is available to Subscribers Only

View Article Abstract & Purchase Options

For full access to this pdf, sign in to an existing account, or purchase an annual subscription.

Subscribe Now