Comparative co-expression analysis in plant biology

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species

(2011) M. Mutwil et al.   PLANT CELL

Dissecting Plant Genomes with the PLAZA Comparative Genomics Platform

(2011) M. Van Bel et al.   PLANT PHYSIOLOGY

Comparative Network Analysis Reveals That Tissue Specificity and Gene Function Are Important Factors Influencing the Mode of Expression Evolution in Arabidopsis and Rice

(2011) S. Movahedi et al.   PLANT PHYSIOLOGY

Gene Coexpression Network Alignment and Conservation of Gene Modules between Two Grass Species: Maize and Rice

(2011) S. P. Ficklin et al.   PLANT PHYSIOLOGY

Plant protein-coding gene families: emerging bioinformatics approaches

(2011) Manuel Martinez   TRENDS IN PLANT SCIENCE

Accurate Quantification of Functional Analogy among Close Homologs

(2011) Maria D. Chikina et al.   PLoS Computational Biology

CoP: a database for characterizing co-expressed gene modules with biological information in plants

(2010) Y. Ogata et al.   BIOINFORMATICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

TobEA: an atlas of tobacco gene expression from seed to senescence

(2010) Kieron D Edwards et al.   BMC GENOMICS

COMODO: an adaptive coclustering strategy to identify conserved coexpression modules between organisms

(2010) Peyman Zarrineh et al.   NUCLEIC ACIDS RESEARCH

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments

(2010) H. Parkinson et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2010) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH

CORNET: A User-Friendly Tool for Data Mining and Integration

(2010) S. De Bodt et al.   PLANT PHYSIOLOGY

Cross-Kingdom Comparison of Transcriptomic Adjustments to Low-Oxygen Stress Highlights Conserved and Plant-Specific Responses

(2010) A. Mustroph et al.   PLANT PHYSIOLOGY

A regulon conserved in monocot and dicot plants defines a functional module in antifungal plant immunity

(2010) M. Humphry et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The MCM-Binding Protein ETG1 Aids Sister Chromatid Cohesion Required for Postreplicative Homologous Recombination Repair

(2010) Naoki Takahashi et al.   PLoS Genetics

Cross species analysis of microarray expression data

(2009) Y. Lu et al.   BIOINFORMATICS

STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data

(2009) Daniel Jupiter et al.   BMC BIOINFORMATICS

A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies

(2009) Yuling Jiao et al.   NATURE GENETICS

KEGG for representation and analysis of molecular networks involving diseases and drugs

(2009) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

(2009) G. Ostlund et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants

(2009) S. Proost et al.   PLANT CELL

A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize

(2009) BJÖRN USADEL et al.   PLANT CELL AND ENVIRONMENT

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

(2009) BJ��RN USADEL et al.   PLANT CELL AND ENVIRONMENT

A dynamic gene expression atlas covering the entire life cycle of rice

(2009) Lei Wang et al.   PLANT JOURNAL

Assembly of an Interactive Correlation Network for the Arabidopsis Genome Using a Novel Heuristic Clustering Algorithm

(2009) M. Mutwil et al.   PLANT PHYSIOLOGY

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

(2009) K. Vandepoele et al.   PLANT PHYSIOLOGY

The flowering world: a tale of duplications

(2009) Yves Van de Peer et al.   TRENDS IN PLANT SCIENCE

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

A cross-species transcriptomics approach to identify genes involved in leaf development

(2008) Nathaniel Street et al.   BMC GENOMICS

Meta Analysis of Gene Expression Data within and Across Species

(2008) Ana Fierro et al.   CURRENT GENOMICS

Hydrogen Peroxide-Induced Gene Expression across Kingdoms: A Comparative Analysis

(2008) K. Vandenbroucke et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Arabidopsis Reactome: A Foundation Knowledgebase for Plant Systems Biology

(2008) N. Tsesmetzis et al.   PLANT CELL

A gene expression atlas of the model legumeMedicago truncatula

(2008) Vagner A. Benedito et al.   PLANT JOURNAL

Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids

(2008) E. Lyons et al.   PLANT PHYSIOLOGY

The quest for orthologs: finding the corresponding gene across genomes

(2008) Arnold Kuzniar et al.   TRENDS IN GENETICS