ReviewJournal of plant research2010
Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways.
Review in Journal of plant research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Arabidopsis MYB47 and MYB95 transcription factors regulate jasmonate-inducible ER-body formation.Communications biology · 2025Article
- Approaches in Gene Coexpression Analysis in Eukaryotes.Biology · 2022Review
- Transcriptome-based approaches for clarification of nutritional responses and improvement of crop production.Breeding science · 2021Article
- ThePlant direct · 2019Article
- Sulphur systems biology-making sense of omics data.Journal of experimental botany · 2019Review
- COXPRESdb v7: a gene coexpression database for 11 animal species supported by 23 coexpression platforms for technical evaluation and evolutionary inference.Nucleic acids research · 2019Article
- ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index.Plant & cell physiology · 2018Article
- GENIUS: web server to predict local gene networks and key genes for biological functions.Bioinformatics (Oxford, England) · 2017Article
- Altered lignification in mur1-1 a mutant deficient in GDP-L-fucose synthesis with reduced RG-II cross linking.PloS one · 2017Article
- Analysis of MAP kinase MPK4/MEKK1/MKK genes of Carica papaya L. comparative to other plant homologues.Bioinformation · 2017Article
- ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression.Plant & cell physiology · 2016Article
- Coexpression Network Analysis of Macronutrient Deficiency Response Genes in Rice.Rice (New York, N.Y.) · 2015Article
- Phylogeny and evolution of plant macrophage migration inhibitory factor/D-dopachrome tautomerase-like proteins.BMC evolutionary biology · 2015Article
- COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems.Nucleic acids research · 2015Article
- Advantages and limitations of shot-gun proteomic analyses on Arabidopsis plants with altered MAPK signaling.Frontiers in plant science · 2015Article
- Identification of Novel Peptidyl Serine α-Galactosyltransferase Gene Family in Plants.The Journal of biological chemistry · 2014Article
- Annotation of gene function in citrus using gene expression information and co-expression networks.BMC plant biology · 2014Article
- Transcriptional responses of Arabidopsis thaliana to chewing and sucking insect herbivores.Frontiers in plant science · 2014Article
- ATTED-II in 2014: evaluation of gene coexpression in agriculturally important plants.Plant & cell physiology · 2014Article
- 2013 awards for Journal of Plant Research publications.Journal of plant research · 2013Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene coexpression analyses are a powerful method to predict the function of genes and/or to identify genes that are functionally related to query genes. The basic idea of gene coexpression analyses is that genes with similar functions should have similar expression patterns under many different conditions. This approach is now widely used by many experimental researchers, especially in the field of plant biology. In this review, we will summarize recent successful examples obtained by using our gene coexpression database, ATTED-II. Specifically, the examples will describe the identification of new genes, such as the subunits of a complex protein, the enzymes in a metabolic pathway and transporters. In addition, we will discuss the discovery of a new intercellular signaling factor and new regulatory relationships between transcription factors and their target genes. In ATTED-II, we provide two basic views of gene coexpression, a gene list view and a gene network view, which can be used as guide gene approach and narrow-down approach, respectively. In addition, we will discuss the coexpression effectiveness for various types of gene sets.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.