(Q34617388)

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Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis

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scholarly article

1 reference

Europe PubMed Central

3 August 2017

Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis (English)

1 reference

Europe PubMed Central

3 August 2017

object named as

James Whelan

7

0 references

author name string

Reena Narsai

1

1 reference

Europe PubMed Central

3 August 2017

James Devenish

2

1 reference

Europe PubMed Central

3 August 2017

Ian Castleden

3

1 reference

Europe PubMed Central

3 August 2017

Kabir Narsai

4

1 reference

Europe PubMed Central

3 August 2017

Lin Xu

5

1 reference

Europe PubMed Central

3 August 2017

Huixia Shou

6

1 reference

Europe PubMed Central

3 August 2017

publication date

29 November 2013

1 reference

Europe PubMed Central

3 August 2017

The Plant Journal

1 reference

Europe PubMed Central

3 August 2017

76

1 reference

Europe PubMed Central

3 August 2017

6

1 reference

Europe PubMed Central

3 August 2017

1057-1073

1 reference

Europe PubMed Central

3 August 2017

OsARG encodes an arginase that plays critical roles in panicle development and grain production in rice

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

MIPS PlantsDB: a database framework for comparative plant genome research

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

RiceFREND: a platform for retrieving coexpressed gene networks in rice

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

RiceXPro version 3.0: expanding the informatics resource for rice transcriptome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

The PRINTS database: a fine-grained protein sequence annotation and analysis resource--its status in 2012

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

Modulation of ethylene responses by OsRTH1 overexpression reveals the biological significance of ethylene in rice seedling growth and development.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

Genome-wide transcriptional profiling of appressorium development by the rice blast fungus Magnaporthe oryzae

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

Massive analysis of rice small RNAs: mechanistic implications of regulated microRNAs and variants for differential target RNA cleavage

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

The Pfam protein families database

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

SMART 7: recent updates to the protein domain annotation resource

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

Homeostatic response to hypoxia is regulated by the N-end rule pathway in plants

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

Defining the protein complex proteome of plant mitochondria

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

PRIN: a predicted rice interactome network

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

OryzaExpress: an integrated database of gene expression networks and omics annotations in rice

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

Common and distinct organ and stress responsive transcriptomic patterns in Oryza sativa and Arabidopsis thaliana

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

Gramene database in 2010: updates and extensions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

AGRIS: the Arabidopsis Gene Regulatory Information Server, an update.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

Plant organelle proteomics: collaborating for optimal cell function.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

YLoc--an interpretable web server for predicting subcellular localization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

Overexpression of the endoplasmic reticulum chaperone BiP3 regulates XA21-mediated innate immunity in rice

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

PROSITE, a protein domain database for functional characterization and annotation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

Mapping metabolic and transcript temporal switches during germination in rice highlights specific transcription factors and the role of RNA instability in the germination process

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

AthaMap, integrating transcriptional and post-transcriptional data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

Systems approaches to identifying gene regulatory networks in plants.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

Towards a better bowl of rice: assigning function to tens of thousands of rice genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

The Rice Annotation Project Database (RAP-DB): 2008 update

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

The Arabidopsis Information Resource (TAIR): gene structure and function annotation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

Functional and evolutionary implications of enhanced genomic analysis of rhomboid intramembrane proteases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

A predicted interactome for Arabidopsis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

WoLF PSORT: protein localization predictor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

Locating proteins in the cell using TargetP, SignalP and related tools

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

GeneBins: a database for classifying gene expression data, with application to plant genome arrays

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

Rice functional genomics research in China

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

PlnTFDB: an integrative plant transcription factor database

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

The rice kinase database. A phylogenomic database for the rice kinome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

The TIGR Rice Genome Annotation Resource: improvements and new features

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

A novel drought-inducible gene, ATAF1, encodes a NAC family protein that negatively regulates the expression of stress-responsive genes in Arabidopsis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

DRTF: a database of rice transcription factors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

Oryzabase. An integrated biological and genome information database for rice

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

Gramene: a bird's eye view of cereal genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

The map-based sequence of the rice genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

GMD@CSB.DB: the Golm Metabolome Database

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

Plant genomics: the third wave.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

The SUPERFAMILY database in 2004: additions and improvements

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

Towards an analysis of the rice mitochondrial proteome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

Sugar modulation of alpha-amylase genes under anoxia

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4253041

7 July 2018

National Science Foundation-Sponsored Workshop Report: "The 2010 Project" functional genomics and the virtual plant. A blueprint for understanding how plants are built and how to improve them.

1 reference

https://api.crossref.org/works/10.1111%2FTPJ.12357

21 January 2018

DCW11, down-regulated gene 11 in CW-type cytoplasmic male sterile rice, encoding mitochondrial protein phosphatase 2c is related to cytoplasmic male sterility.

1 reference

https://api.crossref.org/works/10.1111%2FTPJ.12357

21 January 2018

Detecting and sorting targeting peptides with neural networks and support vector machines.

1 reference

https://api.crossref.org/works/10.1111%2FTPJ.12357

21 January 2018

Combining experimental and predicted datasets for determination of the subcellular location of proteins in Arabidopsis.

1 reference

https://api.crossref.org/works/10.1111%2FTPJ.12357

21 January 2018

Experimental analysis of the rice mitochondrial proteome, its biogenesis, and heterogeneity

1 reference

https://api.crossref.org/works/10.1111%2FTPJ.12357

21 January 2018

High-throughput protein localization in Arabidopsis using Agrobacterium-mediated transient expression of GFP-ORF fusions.

1 reference

https://api.crossref.org/works/10.1111%2FTPJ.12357

21 January 2018

Nucleotide and RNA metabolism prime translational initiation in the earliest events of mitochondrial biogenesis during Arabidopsis germination.

1 reference

https://api.crossref.org/works/10.1111%2FTPJ.12357

21 January 2018

Rice cellulose synthase-like D4 is essential for normal cell-wall biosynthesis and plant growth

1 reference

https://api.crossref.org/works/10.1111%2FTPJ.12357

21 January 2018

Resolving and identifying protein components of plant mitochondrial respiratory complexes using three dimensions of gel electrophoresis.

1 reference

https://api.crossref.org/works/10.1111%2FTPJ.12357

21 January 2018

Prediction of dual protein targeting to plant organelles.

1 reference

https://api.crossref.org/works/10.1111%2FTPJ.12357

21 January 2018

Defining core metabolic and transcriptomic responses to oxygen availability in rice embryos and young seedlings.

1 reference

https://api.crossref.org/works/10.1111%2FTPJ.12357

21 January 2018

In-depth temporal transcriptome profiling reveals a crucial developmental switch with roles for RNA processing and organelle metabolism that are essential for germination in Arabidopsis

1 reference

https://api.crossref.org/works/10.1111%2FTPJ.12357

21 January 2018

Prediction of peroxisomal targeting signal 1 containing proteins from amino acid sequence

1 reference

https://api.crossref.org/works/10.1111%2FTPJ.12357

21 January 2018

Next-generation genetics in plants

1 reference

https://api.crossref.org/works/10.1111%2FTPJ.12357

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1111%2FTPJ.12357

21 January 2018

ARAMEMNON, a novel database for Arabidopsis integral membrane proteins

1 reference

https://api.crossref.org/works/10.1111%2FTPJ.12357

21 January 2018

Predotar: A tool for rapidly screening proteomes for N-terminal targeting sequences

1 reference

https://api.crossref.org/works/10.1111%2FTPJ.12357

21 January 2018

Analysis of the rice mitochondrial carrier family reveals anaerobic accumulation of a basic amino acid carrier involved in arginine metabolism during seed germination

1 reference

https://api.crossref.org/works/10.1111%2FTPJ.12357

21 January 2018

Feeling UPBEAT about Growth: Linking ROS Gradients and Cell Proliferation

1 reference

https://api.crossref.org/works/10.1111%2FTPJ.12357

21 January 2018

Identification of a dual-targeted protein belonging to the mitochondrial carrier family that is required for early leaf development in rice.

1 reference

https://api.crossref.org/works/10.1111%2FTPJ.12357

21 January 2018

Rice 2020: a call for an international coordinated effort in rice functional genomics.

1 reference

https://api.crossref.org/works/10.1111%2FTPJ.12357

21 January 2018

The Mitochondrial Proteome: From Inventory to Function

1 reference

https://api.crossref.org/works/10.1111%2FTPJ.12357

21 January 2018

Metabolite identification via the Madison Metabolomics Consortium Database

1 reference

https://api.crossref.org/works/10.1111%2FTPJ.12357

21 January 2018

EXORDIUM-LIKE1 promotes growth during low carbon availability in Arabidopsis

1 reference

https://pubmed.ncbi.nlm.nih.gov/24147765

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Overexpression of BiP has inhibitory effects on the accumulation of seed storage proteins in endosperm cells of rice

1 reference

https://pubmed.ncbi.nlm.nih.gov/24147765

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

MitoProt, a Macintosh application for studying mitochondrial proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/24147765

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The Botany Array Resource: e-Northerns, Expression Angling, and promoter analyses

1 reference

https://pubmed.ncbi.nlm.nih.gov/24147765

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Rice-specific mitochondrial iron-regulated gene (MIR) plays an important role in iron homeostasis

1 reference

https://pubmed.ncbi.nlm.nih.gov/24147765

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1111/TPJ.12357

1 reference

Europe PubMed Central

3 August 2017

1 reference

Europe PubMed Central

3 August 2017

1 reference

Europe PubMed Central

3 August 2017

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