ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index

Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules

(2017) Colin Ruprecht et al.   PLANT JOURNAL

Why Batch Effects Matter in Omics Data, and How to Avoid Them

(2017) Wilson Wen Bin Goh et al.   TRENDS IN BIOTECHNOLOGY

Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system

(2016) Alexis Vandenbon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Removing Batch Effects from Longitudinal Gene Expression - Quantile Normalization Plus ComBat as Best Approach for Microarray Transcriptome Data

(2016) Christian Müller et al.   PLoS One

Guidance for RNA-seq co-expression network construction and analysis: safety in numbers

(2015) S. Ballouz et al.   BIOINFORMATICS

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

ALCOdb: Gene Coexpression Database for Microalgae

(2015) Yuichi Aoki et al.   PLANT AND CELL PHYSIOLOGY

ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression

(2015) Yuichi Aoki et al.   PLANT AND CELL PHYSIOLOGY

Comparison of Gene Coexpression Profiles and Construction of Conserved Gene Networks to Find Functional Modules

(2015) Yasunobu Okamura et al.   PLoS One

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

ArrayExpress update—simplifying data submissions

(2014) Nikolay Kolesnikov et al.   NUCLEIC ACIDS RESEARCH

Gene: a gene-centered information resource at NCBI

(2014) Garth R. Brown et al.   NUCLEIC ACIDS RESEARCH

ATTED-II in 2014: Evaluation of Gene Coexpression in Agriculturally Important Plants

(2013) Takeshi Obayashi et al.   PLANT AND CELL PHYSIOLOGY

Reuse of public genome-wide gene expression data

(2012) Johan Rung et al.   NATURE REVIEWS GENETICS

DDBJ new system and service refactoring

(2012) Osamu Ogasawara et al.   NUCLEIC ACIDS RESEARCH

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

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

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

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

COXPRESdb: a database to compare gene coexpression in seven model animals

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

Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity

(2009) Koji Kadota et al.   Algorithms for Molecular Biology

Rank of Correlation Coefficient as a Comparable Measure for Biological Significance of Gene Coexpression

(2009) T. Obayashi et al.   DNA RESEARCH

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

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

Conserved co-expression for candidate disease gene prioritization

(2008) Martin Oti et al.   BMC BIOINFORMATICS

The removal of multiplicative, systematic bias allows integration of breast cancer gene expression datasets – improving meta-analysis and prediction of prognosis

(2008) Andrew H Sims et al.   BMC Medical Genomics

ATTED-II provides coexpressed gene networks for Arabidopsis

(2008) T. Obayashi et al.   NUCLEIC ACIDS RESEARCH