ArticleNucleic acids research2017
ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 50 papers, 1 of them a synthesis that pooled it.
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Who cites it
50 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Transcriptional and translational landscape fine-tune genome annotation and explores translation control in cotton.Journal of advanced research · 2024Article
- AlliumDB: a central portal for comparative and functional genomics inHorticulture research · 2024Article
- Identification and characteristics of differentially expressed genes under UV-B stress inFrontiers in plant science · 2024Article
- A comprehensive overview of cotton genomics, biotechnology and molecular biological studies.Science China. Life sciences · 2023Review
- WheatCENet: A Database for Comparative Co-expression Networks Analysis of Allohexaploid Wheat and Its Progenitors.Genomics, proteomics & bioinformatics · 2023Article
- Genome-Wide Investigation and Co-Expression Network Analysis of SBT Family Gene inInternational journal of molecular sciences · 2023Article
- CottonMD: a multi-omics database for cotton biological study.Nucleic acids research · 2023Article
- Flame resistant cotton lines generated by synergistic epistasis in a MAGIC population.PloS one · 2023Article
- Improvement of plant tolerance to drought stress by cotton tubby-like protein 30 through stomatal movement regulation.Journal of advanced research · 2022Article
- A deletion/duplication in the Ligon lintless-2 locus induces siRNAs that inhibit cotton fiber cell elongation.Plant physiology · 2022Article
- A Comprehensive Gene Co-Expression Network Analysis Reveals a Role ofInternational journal of molecular sciences · 2022Article
- COTTONOMICS: a comprehensive cotton multi-omics database.Database : the journal of biological databases and curation · 2022Article
- Analyzing lignin biosynthesis pathways in rattan using improved co-expression networks of NACs and MYBs.BMC plant biology · 2022Article
- APE1 controls DICER1 expression in NSCLC through miR-33a and miR-130b.Cellular and molecular life sciences : CMLS · 2022Article
- Enhanced seedling growth by 3-Plant direct · 2022Article
Corrections and comments
- Erratum issued
Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Plant genera with both diploid and polyploid species are a common evolutionary occurrence. Polyploids, especially allopolyploids such as cotton and wheat, are a great model system for heterosis research. Here, we have integrated genome sequences and transcriptome data of Gossypium species to construct co-expression networks and identified functional modules from different cotton species, including 1155 and 1884 modules in G. arboreum and G. hirsutum, respectively. We overlayed the gene expression results onto the co-expression network. We further provided network comparison analysis for orthologous genes across the diploid and allotetraploid Gossypium We also constructed miRNA-target networks and predicted PPI networks for both cotton species. Furthermore, we integrated in-house ChIP-seq data of histone modification (H3K4me3) together with cis-element analysis and gene sets enrichment analysis tools for studying possible gene regulatory mechanism in Gossypium species. Finally, we have constructed an online ccNET database (http://structuralbiology.cau.edu.cn/gossypium) for comparative gene functional analyses at a multi-dimensional network and epigenomic level across diploid and polyploid Gossypium species. The ccNET database will be beneficial for community to yield novel insights into gene/module functions during cotton development and stress response, and might be useful for studying conservation and diversity in other polyploid plants, such as T. aestivum and Brassica napus.
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Registered trials
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.