ArticlePlant & cell physiology2014
ATTED-II in 2014: evaluation of gene coexpression in agriculturally important plants.
Article in Plant & cell physiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
- An Introduction to Network Analysis in Plant Biology.Plant direct · 2025Article
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- PlantNexus: A Gene Co-expression Network Database and Visualization Tool for Barley and Sorghum.Plant & cell physiology · 2022Article
- Cellular export of sugars and amino acids: role in feeding other cells and organisms.Plant physiology · 2021Review
- Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture.EMBO reports · 2021Article
- Araport Lives: An Updated Framework for Arabidopsis Bioinformatics.The Plant cell · 2020Article
- Gene Regulatory Network Inference: Connecting Plant Biology and Mathematical Modeling.Frontiers in genetics · 2020Review
- A member of the CONSTANS-Like protein family is a putative regulator of reactive oxygen species homeostasis and spaceflight physiological adaptation.AoB PLANTS · 2019Article
- Pan- and core- gene association networks: Integrative approaches to understanding biological regulation.PloS one · 2019Article
- Rice Genome-Scale Network Integration Reveals Transcriptional Regulators of Grass Cell Wall Synthesis.Frontiers in plant science · 2019Article
- Gene networks underlying the early regulation of Paraburkholderia phytofirmans PsJN induced systemic resistance in Arabidopsis.PloS one · 2019Article
- Integrating Coexpression Networks with GWAS to Prioritize Causal Genes in Maize.The Plant cell · 2018Article
- Identification of Key Enzymes for Pectin Synthesis in Seed Mucilage.Plant physiology · 2018Article
- REBELOTE, a regulator of floral determinacy inFEBS open bio · 2018Article
- ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index.Plant & cell physiology · 2018Article
- Ethylene Receptors Signal via a Noncanonical Pathway to Regulate Abscisic Acid Responses.Plant physiology · 2018Article
- The Plastid and Mitochondrial Peptidase Network inThe Plant cell · 2017Review
- SIEVE ELEMENT-LINING CHAPERONE1 Restricts Aphid Feeding on Arabidopsis during Heat Stress.The Plant cell · 2017Article
- Light Controls Cytokinin Signaling via Transcriptional Regulation of Constitutively Active Sensor Histidine Kinase CKI1.Plant physiology · 2017Article
- Skewing in Arabidopsis roots involves disparate environmental signaling pathways.BMC plant biology · 2017Article
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7 authors.
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Abstract
ATTED-II (http://atted.jp) is a database of coexpressed genes that was originally developed to identify functionally related genes in Arabidopsis and rice. Herein, we describe an updated version of ATTED-II, which expands this resource to include additional agriculturally important plants. To improve the quality of the coexpression data for Arabidopsis and rice, we included more gene expression data from microarray and RNA sequencing studies. The RNA sequencing-based coexpression data now cover 94% of the Arabidopsis protein-encoding genes, representing a substantial increase from previously available microarray-based coexpression data (76% coverage). We also generated coexpression data for four dicots (soybean, poplar, grape and alfalfa) and one monocot (maize). As both the quantity and quality of expression data for the non-model species are generally poorer than for the model species, we verified coexpression data associated with these new species using multiple methods. First, the overall performance of the coexpression data was evaluated using gene ontology annotations and the coincidence of a genomic feature. Secondly, the reliability of each guide gene was determined by comparing coexpressed gene lists between platforms. With the expanded and newly evaluated coexpression data, ATTED-II represents an important resource for identifying functionally related genes in agriculturally important plants.
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