Learning from co-expression networks: possibilities and challenges

EAR Serin, H Nijveen, HWM Hilhorst… - Frontiers in plant …, 2016 - frontiersin.org
Plants are fascinating and complex organisms. A comprehensive understanding of the
organization, function and evolution of plant genes is essential to disentangle important …

Reuse of public genome-wide gene expression data

J Rung, A Brazma - Nature Reviews Genetics, 2013 - nature.com
Our understanding of gene expression has changed dramatically over the past decade,
largely catalysed by technological developments. High-throughput experiments …

Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics

H Sakai, SS Lee, T Tanaka, H Numa… - Plant and Cell …, 2013 - academic.oup.com
Abstract The Rice Annotation Project Database (RAP-DB, http://rapdb. dna. affrc. go. jp/) has
been providing a comprehensive set of gene annotations for the genome sequence of rice …

Integrated omics analysis of specialized metabolism in medicinal plants

A Rai, K Saito, M Yamazaki - The Plant Journal, 2017 - Wiley Online Library
Medicinal plants are a rich source of highly diverse specialized metabolites with important
pharmacological properties. Until recently, plant biologists were limited in their ability to …

RiceXPro version 3.0: expanding the informatics resource for rice transcriptome

Y Sato, H Takehisa, K Kamatsuki, H Minami… - Nucleic acids …, 2013 - academic.oup.com
A wide range of resources on gene expression profiling enhance various strategies in plant
molecular biology particularly in characterization of gene function. We have updated our …

Rice Expression Database (RED): An integrated RNA-Seq-derived gene expression database for rice

L Xia, D Zou, J Sang, X Xu, H Yin, M Li, S Wu… - Journal of Genetics and …, 2017 - Elsevier
Rice is one of the most important stable food as well as a monocotyledonous model
organism for the plant research community. Here, we present RED (Rice Expression …

Advances in omics and bioinformatics tools for systems analyses of plant functions

K Mochida, K Shinozaki - Plant and Cell Physiology, 2011 - academic.oup.com
Omics and bioinformatics are essential to understanding the molecular systems that underlie
various plant functions. Recent game-changing sequencing technologies have revitalized …

The plant ontology as a tool for comparative plant anatomy and genomic analyses

L Cooper, RL Walls, J Elser, MA Gandolfo… - Plant and Cell …, 2013 - academic.oup.com
Abstract The Plant Ontology (PO; http://www. plantontology. org/) is a publicly available,
collaborative effort to develop and maintain a controlled, structured vocabulary ('ontology') of …

Cytosolic glutamine synthetase1; 2 is responsible for the primary assimilation of ammonium in rice roots

K Funayama, S Kojima… - Plant and cell …, 2013 - academic.oup.com
Among three genes for cytosolic glutamine synthetase (OsGS1; 1, OsGS1; 2 and OsGS1; 3)
in rice (Oryza sativa L.) plants, the OsGS1; 2 gene is known to be mainly expressed in …

The rice oligonucleotide array database: an atlas of rice gene expression

P Cao, KH Jung, D Choi, D Hwang, J Zhu, PC Ronald - Rice, 2012 - Springer
Background Microarray technologies facilitate high-throughput gene expression analysis.
However, the diversity of platforms for rice gene expression analysis hinders efficient …