ArticlePlant & cell physiology2018
ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index.
Article in Plant & cell physiology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 106 papers, 2 of them syntheses that pooled it.
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Who cites it
106 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- A comparative meta-proteomic pipeline for the identification of plasmodesmata proteins and regulatory conditions in diverse plant species.BMC biology · 2022Pooled it
- Network aggregation improves gene function prediction of grapevine gene co-expression networks.Plant molecular biology · 2020Pooled it
- Evolutionary Divergence, Predicted Interaction Interface, and Regulatory Specialization of MTB as a Non-Catalytic Scaffold in the Plant m6A Writer Complex.Current issues in molecular biology · 2026Article
- Chromatin state architecture governs transcription factor accessibility across plant genomes.PLoS genetics · 2026Article
- SUPPRESSOR OF LAZY QUADRUPLE 1 acts at ER-plasma membrane contact sites to control a gravitropism pathway in theProceedings of the National Academy of Sciences of the United States of America · 2025Article
- An Introduction to Network Analysis in Plant Biology.Plant direct · 2025Article
- Comparative Transcriptome Reveals Conserved Gene Expression in Reproductive Organs in Solanaceae.International journal of molecular sciences · 2025Article
- Co-option and neofunctionalization of stomatal executors for defence against herbivores in Brassicales.Nature plants · 2025Article
- ACT2.6: Global Gene Coexpression Network inGenes · 2025Article
- Pan-Genome-Wide Investigation and Co-Expression Network Analysis ofInternational journal of molecular sciences · 2024Article
- Altered Metabolism in Knockdown Lines of Two HXXXD/BAHD Acyltransferases During Wound Healing in Potato Tubers.Plants (Basel, Switzerland) · 2024Article
- NKS1/ELMO4 is an integral protein of a pectin synthesis protein complex and maintains Golgi morphology and cell adhesion inProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Auxin and carbohydrate control flower bud development in Anthurium andraeanum during early stage of sexual reproduction.BMC plant biology · 2024Article
- Small secreted proteins and exocytosis regulators: do they go along?Plant signaling & behavior · 2023Article
- Coordinated regulation of the entry and exit steps of aromatic amino acid biosynthesis supports the dual lignin pathway in grasses.Nature communications · 2023Article
- The Progression in Developing Genomic Resources for Crop Improvement.Life (Basel, Switzerland) · 2023Review
- Sensory plastid-associated PsbP DOMAIN-CONTAINING PROTEIN 3 triggers plant growth- and defense-related epigenetic responses.The Plant journal : for cell and molecular biology · 2023Article
- An ancient metabolite damage-repair system sustains photosynthesis in plants.Nature communications · 2023Article
- Comparative Coexpression Analysis of Indole Synthase and Tryptophan Synthase A Reveals the Independent Production of Auxin via the Cytosolic Free Indole.Plants (Basel, Switzerland) · 2023Article
- Genome-Wide Investigation and Co-Expression Network Analysis of SBT Family Gene inInternational journal of molecular sciences · 2023Article
46 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
ATTED-II (http://atted.jp) is a coexpression database for plant species to aid in the discovery of relationships of unknown genes within a species. As an advanced coexpression analysis method, multispecies comparisons have the potential to detect alterations in gene relationships within an evolutionary context. However, determining the validity of comparative coexpression studies is difficult without quantitative assessments of the quality of coexpression data. ATTED-II (version 9) provides 16 coexpression platforms for nine plant species, including seven species supported by both microarray- and RNA sequencing (RNAseq)-based coexpression data. Two independent sources of coexpression data enable the assessment of the reproducibility of coexpression. The latest coexpression data for Arabidopsis (Ath-m.c7-1 and Ath-r.c3-0) showed the highest reproducibility (Jaccard coefficient = 0.13) among previous coexpression data in ATTED-II. We also investigated the statistical basis of the mutual rank (MR) index as a coexpression measure by bootstrap sampling of experimental units. We found that the error distribution of the logit-transformed MR index showed normality with equal variances for each coexpression platform. Because the MR error was strongly correlated with the number of samples for the coexpression data, typical confidence intervals for the MR index can be estimated for any coexpression platform. These new, high-quality coexpression data can be analyzed with any tool in ATTED-II and combined with external resources to obtain insight into plant biology.
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