Comparative analyses of stress-responsive genes in Arabidopsis thaliana: insight from genomic data mining, functional enrichment, pathway analysis and phenomics

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

(2013) Mahantesha Naika et al.   PLANT AND CELL PHYSIOLOGY

Effects of abiotic stress on plants: a systems biology perspective

(2012) Grant R Cramer et al.   BMC PLANT BIOLOGY

The interaction of plant biotic and abiotic stresses: from genes to the field

(2012) N. J. Atkinson et al.   JOURNAL OF EXPERIMENTAL BOTANY

Drought, salt, and temperature stress-induced metabolic rearrangements and regulatory networks

(2012) J. Krasensky et al.   JOURNAL OF EXPERIMENTAL BOTANY

CDD: conserved domains and protein three-dimensional structure

(2012) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Systematic Identification of Functional Plant Modules through the Integration of Complementary Data Sources

(2012) K. S. Heyndrickx et al.   PLANT PHYSIOLOGY

Structural and Functional Analysis of VQ Motif-Containing Proteins in Arabidopsis as Interacting Proteins of WRKY Transcription Factors

(2012) Y. Cheng et al.   PLANT PHYSIOLOGY

Characterization of the Nrt2.6 Gene in Arabidopsis thaliana: A Link with Plant Response to Biotic and Abiotic Stress

(2012) Julie Dechorgnat et al.   PLoS One

Dynamic differential methylation facilitates pathogen stress response in Arabidopsis

(2012) X. Zhang   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants

(2011) Basel Khraiwesh et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Polyamines: Natural and engineered abiotic and biotic stress tolerance in plants

(2011) Syed Sarfraz Hussain et al.   BIOTECHNOLOGY ADVANCES

Combining literature text mining with microarray data: advances for system biology modeling

(2011) A. Faro et al.   BRIEFINGS IN BIOINFORMATICS

Genetic analysis of abiotic stress tolerance in crops

(2011) Stuart J Roy et al.   CURRENT OPINION IN PLANT BIOLOGY

Plant proteome changes under abiotic stress — Contribution of proteomics studies to understanding plant stress response

(2011) Klára Kosová et al.   Journal of Proteomics

PASS2 version 4: An update to the database of structure-based sequence alignments of structural domain superfamilies

(2011) A. Gandhimathi et al.   NUCLEIC ACIDS RESEARCH

The UniProt-GO Annotation database in 2011

(2011) E. C. Dimmer et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Arabidopsis Seed Germination Under Abiotic Stress as a Concert of Action of Phytohormones

(2011) Agata Daszkowska-Golec   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Transcription Regulation of Abiotic Stress Responses in Rice: A Combined Action of Transcription Factors and Epigenetic Mechanisms

(2011) Ana Paula Santos et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

An Omics Approach to Understand the Plant Abiotic Stress

(2011) Mousumi Debnath et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Interactions between Polyamines and Abiotic Stress Pathway Responses Unraveled by Transcriptome Analysis of Polyamine Overproducers

(2011) Francisco Marco et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Coordinated Gene Networks RegulatingArabidopsisPlant Metabolism in Response to Various Stresses and Nutritional Cues

(2011) Hadar Less et al.   PLANT CELL

Quantitative transcriptomic analysis of abscisic acid-induced and reactive oxygen species-dependent expression changes and proteomic profiling in Arabidopsis suspension cells

(2011) Maik Böhmer et al.   PLANT JOURNAL

Early Transcriptional Defense Responses in Arabidopsis Cell Suspension Culture under High-Light Conditions

(2011) S. Gonzalez-Perez et al.   PLANT PHYSIOLOGY

Current advances in the investigation of leaf rolling caused by biotic and abiotic stress factors

(2011) Asim Kadioglu et al.   PLANT SCIENCE

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Cis-regulatory code of stress-responsive transcription in Arabidopsis thaliana

(2011) C. Zou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phenomics – technologies to relieve the phenotyping bottleneck

(2011) Robert T. Furbank et al.   TRENDS IN PLANT SCIENCE

Improved predictions by Pcons.net using multiple templates

(2010) P. Larsson et al.   BIOINFORMATICS

Low-complexity regions within protein sequences have position-dependent roles

(2010) Alain Coletta et al.   BMC Systems Biology

‘Omics’ analyses of regulatory networks in plant abiotic stress responses

(2010) Kaoru Urano et al.   CURRENT OPINION IN PLANT BIOLOGY

Genetic and genomic tools to improve drought tolerance in wheat

(2010) D. Fleury et al.   JOURNAL OF EXPERIMENTAL BOTANY

Molecular Mechanisms Regulating Rapid Stress Signaling Networks inArabidopsis

(2010) Justin W. Walley et al.   Journal of Integrative Plant Biology

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

The bHLH Transcription Factor POPEYE Regulates Response to Iron Deficiency in Arabidopsis Roots

(2010) T. A. Long et al.   PLANT CELL

Research on plant abiotic stress responses in the post-genome era: past, present and future

(2010) Takashi Hirayama et al.   PLANT JOURNAL

Molecular and Physiological Analysis of Drought Stress in Arabidopsis Reveals Early Responses Leading to Acclimation in Plant Growth

(2010) A. Harb et al.   PLANT PHYSIOLOGY

Polyamines: molecules with regulatory functions in plant abiotic stress tolerance

(2010) Rubén Alcázar et al.   PLANTA

Natural Variation in Arabidopsis thaliana Revealed a Genetic Network Controlling Germination Under Salt Stress

(2010) Navot Galpaz et al.   PLoS One

Finding the Right Questions: Exploratory Pathway Analysis to Enhance Biological Discovery in Large Datasets

(2010) Thomas Kelder et al.   PLOS BIOLOGY

Tissue-specific regulation of rice molybdenum cofactor sulfurase gene in response to salt stress and ABA

(2009) Ping-Min Huang et al.   ACTA PHYSIOLOGIAE PLANTARUM

Comparing gene annotation enrichment tools for functional modeling of agricultural microarray data

(2009) Bart Berg et al.   BMC BIOINFORMATICS

Omics meet networks—using systems approaches to infer regulatory networks in plants

(2009) Miguel A Moreno-Risueno et al.   CURRENT OPINION IN PLANT BIOLOGY

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Phenylpropanoid Biosynthesis

(2009) Thomas Vogt   Molecular Plant

Protein structure prediction on the Web: a case study using the Phyre server

(2009) Lawrence A Kelley et al.   Nature Protocols

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

G-SESAME: web tools for GO-term-based gene similarity analysis and knowledge discovery

(2009) Z. Du et al.   NUCLEIC ACIDS RESEARCH

BioMart Central Portal—unified access to biological data

(2009) Syed Haider et al.   NUCLEIC ACIDS RESEARCH

Auxin Response in Arabidopsis under Cold Stress: Underlying Molecular Mechanisms

(2009) K. Shibasaki et al.   PLANT CELL

Transcriptional Regulatory Networks in Response to Abiotic Stresses in Arabidopsis and Grasses

(2009) K. Nakashima et al.   PLANT PHYSIOLOGY

Mapping genes for plant structure, development and evolution: functional mapping meets ontology

(2009) Qiuling He et al.   TRENDS IN GENETICS

Photosynthesis under drought and salt stress: regulation mechanisms from whole plant to cell

(2008) M. M. Chaves et al.   ANNALS OF BOTANY

Systems Approaches to Identifying Gene Regulatory Networks in Plants

(2008) Terri A. Long et al.   Annual Review of Cell and Developmental Biology

Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration

(2008) S. Bauer et al.   BIOINFORMATICS

Nitric oxide, stomatal closure, and abiotic stress

(2008) S. Neill et al.   JOURNAL OF EXPERIMENTAL BOTANY

Abscisic Acid-mediated Epigenetic Processes in Plant Development and Stress Responses

(2008) Viswanathan Chinnusamy et al.   Journal of Integrative Plant Biology

The future of biocuration

(2008) Doug Howe et al.   NATURE

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Arabidopsis Transcriptome Analysis under Drought, Cold, High-Salinity and ABA Treatment Conditions using a Tiling Array

(2008) A. Matsui et al.   PLANT AND CELL PHYSIOLOGY

Metabolic regulation of leaf senescence: interactions of sugar signalling with biotic and abiotic stress responses

(2008) A. Wingler et al.   PLANT BIOLOGY

Arabidopsis PPR40 Connects Abiotic Stress Responses to Mitochondrial Electron Transport

(2008) L. Zsigmond et al.   PLANT PHYSIOLOGY

Polyamines: essential factors for growth and survival

(2008) T. Kusano et al.   PLANTA

Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana

(2008) H.-H. Liu et al.   RNA

Advanced Genomic Data Mining

(2008) Xosé M. Fernández-Suárez et al.   PLoS Computational Biology