ArticlePlant & cell physiology2016
ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression.
Article in Plant & cell physiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers, 1 of them a synthesis that pooled it.
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Who cites it
81 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Network aggregation improves gene function prediction of grapevine gene co-expression networks.Plant molecular biology · 2020Pooled it
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- Transcriptional and translational landscape fine-tune genome annotation and explores translation control in cotton.Journal of advanced research · 2024Article
- ARSK1 activates TORC1 signaling to adjust growth to phosphate availability in Arabidopsis.Current biology : CB · 2023Article
- WheatCENet: A Database for Comparative Co-expression Networks Analysis of Allohexaploid Wheat and Its Progenitors.Genomics, proteomics & bioinformatics · 2023Article
- Multi-Omics Approaches and Resources for Systems-Level Gene Function Prediction in the Plant Kingdom.Plants (Basel, Switzerland) · 2022Review
- Patterns of pan-genome occupancy and gene coexpression under water-deficit in Brachypodium distachyon.Molecular ecology · 2022Article
- PlantNexus: A Gene Co-expression Network Database and Visualization Tool for Barley and Sorghum.Plant & cell physiology · 2022Article
- Identification of Potential Genes Encoding Protein Transporters inLife (Basel, Switzerland) · 2022Article
- Research Advances and Prospects of Orphan Genes in Plants.Frontiers in plant science · 2022Review
- Comparative RNA-Seq analysis of the root revealed transcriptional regulation system for aluminum tolerance in contrasting indica rice of North East India.Protoplasma · 2021Article
- ADAP is a possible negative regulator of glucosinolate biosynthesis in Arabidopsis thaliana based on clustering and gene expression analyses.Journal of plant research · 2021Article
- The evolutionary conserved iron-sulfur protein TCR controls P700 oxidation in photosystem I.iScience · 2021Article
- PotentialPeerJ · 2021Article
- CLE2 regulates light-dependent carbohydrate metabolism in Arabidopsis shoots.Plant molecular biology · 2020Article
- Auxin apical dominance governed by the OsAsp1-OsTIF1 complex determines distinctive rice caryopses development on different branches.PLoS genetics · 2020Article
- MyoMiner: explore gene co-expression in normal and pathological muscle.BMC medical genomics · 2020Article
- Using Gene Expression to Study Specialized Metabolism-A Practical Guide.Frontiers in plant science · 2020Review
21 more citing papers are in PubMed but not listed here.
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5 authors.
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Abstract
ATTED-II (http://atted.jp) is a coexpression database for plant species with parallel views of multiple coexpression data sets and network analysis tools. The user can efficiently find functional gene relationships and design experiments to identify gene functions by reverse genetics and general molecular biology techniques. Here, we report updates to ATTED-II (version 8.0), including new and updated coexpression data and analysis tools. ATTED-II now includes eight microarray- and six RNA sequencing-based coexpression data sets for seven dicot species (Arabidopsis, field mustard, soybean, barrel medick, poplar, tomato and grape) and two monocot species (rice and maize). Stand-alone coexpression analyses tend to have low reliability. Therefore, examining evolutionarily conserved coexpression is a more effective approach from the viewpoints of reliability and evolutionary importance. In contrast, the reliability of species-specific coexpression data remains poor. Our assessment scores for individual coexpression data sets indicated that the quality of the new coexpression data sets in ATTED-II is higher than for any previous coexpression data set. In addition, five species (Arabidopsis, soybean, tomato, rice and maize) in ATTED-II are now supported by both microarray- and RNA sequencing-based coexpression data, which has increased the reliability. Consequently, ATTED-II can now provide lineage-specific coexpression information. As an example of the use of ATTED-II to explore lineage-specific coexpression, we demonstrate monocot- and dicot-specific coexpression of cell wall genes. With the expanded coexpression data for multilevel evaluation, ATTED-II provides new opportunities to investigate lineage-specific evolution in plants.
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