ArticleThe Plant cell2011
PlaNet: combined sequence and expression comparisons across plant networks derived from seven species.
Article in The Plant cell, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 155 papers, 1 of them a synthesis that pooled it.
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Who cites it
155 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Data integration through proximity-based networks provides biological principles of organization across scales.The Plant cell · 2013Pooled it
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- Growing connections: PlantConnectome maps molecular networks in Arabidopsis.The Plant cell · 2025Article
- Cross-species analysis of abiotic stress in hydroponic leafy crops reveals conserved regulatory networks and key divergences.Frontiers in plant science · 2025Article
- Altered Metabolism in Knockdown Lines of Two HXXXD/BAHD Acyltransferases During Wound Healing in Potato Tubers.Plants (Basel, Switzerland) · 2024Article
- A gene network-driven approach to infer novel pathogenicity-associated genes: application tomSystems · 2023Article
- MYB24 orchestrates terpene and flavonol metabolism as light responses to anthocyanin depletion in variegated grape berries.The Plant cell · 2023Article
- The Rauvolfia tetraphylla genome suggests multiple distinct biosynthetic routes for yohimbane monoterpene indole alkaloids.Communications biology · 2023Article
- Comparative single-cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution.Nature ecology & evolution · 2023Article
- Plant biochemical genetics in the multiomics era.Journal of experimental botany · 2023Review
- A Survey of the Transcriptomic Resources in Durum Wheat: Stress Responses, Data Integration and Exploitation.Plants (Basel, Switzerland) · 2023Review
- From Classical to Modern Computational Approaches to Identify Key Genetic Regulatory Components in Plant Biology.International journal of molecular sciences · 2023Review
- Interspecific comparison of gene expression profiles using machine learning.PLoS computational biology · 2023Article
- Evolutionary analysis of the LORELEI gene family in plants reveals regulatory subfunctionalization.Plant physiology · 2022Article
- Identification of growth regulators using cross-species network analysis in plants.Plant physiology · 2022Article
- Rice OsPUB16 modulates the 'SAPK9-OsMADS23-OsAOC' pathway to reduce plant water-deficit tolerance by repressing ABA and JA biosynthesis.PLoS genetics · 2022Article
- Multi-Omics Approaches and Resources for Systems-Level Gene Function Prediction in the Plant Kingdom.Plants (Basel, Switzerland) · 2022Review
95 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The model organism Arabidopsis thaliana is readily used in basic research due to resource availability and relative speed of data acquisition. A major goal is to transfer acquired knowledge from Arabidopsis to crop species. However, the identification of functional equivalents of well-characterized Arabidopsis genes in other plants is a nontrivial task. It is well documented that transcriptionally coordinated genes tend to be functionally related and that such relationships may be conserved across different species and even kingdoms. To exploit such relationships, we constructed whole-genome coexpression networks for Arabidopsis and six important plant crop species. The interactive networks, clustered using the HCCA algorithm, are provided under the banner PlaNet (http://aranet.mpimp-golm.mpg.de). We implemented a comparative network algorithm that estimates similarities between network structures. Thus, the platform can be used to swiftly infer similar coexpressed network vicinities within and across species and can predict the identity of functional homologs. We exemplify this using the PSA-D and chalcone synthase-related gene networks. Finally, we assessed how ontology terms are transcriptionally connected in the seven species and provide the corresponding MapMan term coexpression networks. The data support the contention that this platform will considerably improve transfer of knowledge generated in Arabidopsis to valuable crop species.
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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.