AtPAN: an integrated system for reconstructing transcriptional regulatory networks in Arabidopsis thaliana

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

Using Unsupervised Patterns to Extract Gene Regulation Relationships for Network Construction

(2011) Yi-Tsung Tang et al.   PLoS One

Combinatorial regulation of transcription factors and microRNAs

(2010) Naifang Su et al.   BMC Systems Biology

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

PAIR: the predicted Arabidopsis interactome resource

(2010) Mingzhi Lin et al.   NUCLEIC ACIDS RESEARCH

AGRIS: the Arabidopsis Gene Regulatory Information Server, an update

(2010) A. Yilmaz et al.   NUCLEIC ACIDS RESEARCH

The BioGRID Interaction Database: 2011 update

(2010) C. Stark et al.   NUCLEIC ACIDS RESEARCH

Entrez Gene: gene-centered information at NCBI

(2010) D. Maglott et al.   NUCLEIC ACIDS RESEARCH

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

(2010) David Warde-Farley et al.   NUCLEIC ACIDS RESEARCH

Mechanisms independent of abscisic acid (ABA) or proline feedback have a predominant role in transcriptional regulation of proline metabolism during low water potential and stress recovery

(2010) SANDEEP SHARMA et al.   PLANT CELL AND ENVIRONMENT

Integrated omics approaches in plant systems biology

(2009) Atsushi Fukushima et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks

(2009) K. Vandepoele et al.   PLANT PHYSIOLOGY

PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups

(2008) Wen-Chi Chang et al.   BMC GENOMICS

AthaMap, integrating transcriptional and post-transcriptional data

(2008) L. Bulow et al.   NUCLEIC ACIDS RESEARCH

Decoding genes with coexpression networks and metabolomics – ‘majority report by precogs’

(2007) Kazuki Saito et al.   TRENDS IN PLANT SCIENCE