ArticleNucleic acids research2018
CoNekT: an open-source framework for comparative genomic and transcriptomic network analyses.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers, 2 of them syntheses that pooled it.
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61 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Early "Rootprints" of Plant Terrestrialization: Selaginella Root Development Sheds Light on Root Evolution in Vascular Plants.Frontiers in plant science · 2021Pooled it
- Network aggregation improves gene function prediction of grapevine gene co-expression networks.Plant molecular biology · 2020Pooled it
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- Constructing gene co-functional and co-regulatory networks from public transcriptomes using condition-specific ensemble co-expression.Nature communications · 2026Article
- PharaohFUN: phylogenomic analysis for plant protein history and function elucidation.Molecular biology and evolution · 2026Article
- Genome-wide association study for root-related traits at vegetative growth stages of soybean (Glycine max L. Merrill).BMC genomics · 2026Article
- Big data approaches to understanding gene regulatory networks in the shoot apical meristem andFrontiers in plant science · 2026Review
- Tomato pollen tube growth requires flavonol glycosylation.Plant physiology · 2025Article
- Function and evolution of plant annexins in response to abiotic stresses.BMC plant biology · 2025Review
- Molecular Evolution of Plant SULTR Proteins and Expression Analysis of HvSULTR Under Heat Stress in Barley.Plants (Basel, Switzerland) · 2025Article
- Growing connections: PlantConnectome maps molecular networks in Arabidopsis.The Plant cell · 2025Article
- Algal origins of core land plant stress response subnetworks.The Plant journal : for cell and molecular biology · 2025Article
- Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls.Nature plants · 2025Article
- New QTLs involved in the control of stigma position in tomato.BMC plant biology · 2025Article
- Biosynthesis and Physiological Significance of Organ-Specific Flavonol Glycosides in Solanaceae.bioRxiv : the preprint server for biology · 2025Article
- Cropformer: An interpretable deep learning framework for crop genomic prediction.Plant communications · 2025Article
- Sporophyte-directed gametogenesis in Arabidopsis.Nature plants · 2025Article
- Genome-Wide Identification, Molecular Evolution, and Expression Divergence ofFood science & nutrition · 2025Article
1 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
The recent accumulation of gene expression data in the form of RNA sequencing creates unprecedented opportunities to study gene regulation and function. Furthermore, comparative analysis of the expression data from multiple species can elucidate which functional gene modules are conserved across species, allowing the study of the evolution of these modules. However, performing such comparative analyses on raw data is not feasible for many biologists. Here, we present CoNekT (Co-expression Network Toolkit), an open source web server, that contains user-friendly tools and interactive visualizations for comparative analyses of gene expression data and co-expression networks. These tools allow analysis and cross-species comparison of (i) gene expression profiles; (ii) co-expression networks; (iii) co-expressed clusters involved in specific biological processes; (iv) tissue-specific gene expression; and (v) expression profiles of gene families. To demonstrate these features, we constructed CoNekT-Plants for green alga, seed plants and flowering plants (Picea abies, Chlamydomonas reinhardtii, Vitis vinifera, Arabidopsis thaliana, Oryza sativa, Zea mays and Solanum lycopersicum) and thus provide a web-tool with the broadest available collection of plant phyla. CoNekT-Plants is freely available from http://conekt.plant.tools, while the CoNekT source code and documentation can be found at https://github.molgen.mpg.de/proost/CoNekT/.
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