ArticleScientific reports2016
Co-expression network analyses identify functional modules associated with development and stress response in Gossypium arboreum.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 40 citations in OpenAlex.
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- A Comprehensive Gene Co-Expression Network Analysis Reveals a Role ofInternational journal of molecular sciences · 2022Article
- Multi-Omics Approaches and Resources for Systems-Level Gene Function Prediction in the Plant Kingdom.Plants (Basel, Switzerland) · 2022Review
- Analyzing lignin biosynthesis pathways in rattan using improved co-expression networks of NACs and MYBs.BMC plant biology · 2022Article
- Transcriptome-guided annotation and functional classification of long non-coding RNAs in Arabidopsis thaliana.Scientific reports · 2022Article
- Transcriptome and Resequencing Analyses Provide Insight into Differences in Organic Acid Accumulation in Two Pear Varieties.International journal of molecular sciences · 2021Article
- Genome-Wide Mining of MYB Transcription Factors in the Anthocyanin Biosynthesis Pathway of Gossypium Hirsutum.Biochemical genetics · 2021Article
- Topological clustering of regulatory genes confers pathogenic tolerance to cassava brown streak virus (CBSV) in cassava.Scientific reports · 2021Article
- PSDX: A Comprehensive Multi-Omics Association Database ofFrontiers in plant science · 2021Article
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- Coexpression Analysis Reveals Dynamic Modules Regulating the Growth and Development of Cirri in the Rattans (Frontiers in genetics · 2020Article
- Transcriptional Profiling Reveals a Time-of-Day-Specific Role of REVEILLE 4/8 in Regulating the First Wave of Heat Shock-Induced Gene Expression in Arabidopsis.The Plant cell · 2019Article
- Integrating data and knowledge to identify functional modules of genes: a multilayer approach.BMC bioinformatics · 2019Article
- croFGD:Frontiers in genetics · 2019Article
- Global transcriptome and weighted gene co-expression network analyses reveal hybrid-specific modules and candidate genes related to plant height development in maize.Plant molecular biology · 2018Article
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- PCSD: a plant chromatin state database.Nucleic acids research · 2018Article
- Co-expression Gene Network Analysis and Functional Module Identification in Bamboo Growth and Development.Frontiers in genetics · 2018Article
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Authors and funding
12 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cotton is an economically important crop, essential for the agriculture and textile industries. Through integrating transcriptomic data, we discovered that multi-dimensional co-expression network analysis was powerful for predicting cotton gene functions and functional modules. Here, the recently available transcriptomic data on Gossypium arboreum, including data on multiple growth stages of tissues and stress treatment samples were applied to construct a co-expression network exploring multi-dimensional expression (development and stress) through multi-layered approaches. Based on differential gene expression and network analysis, a fibre development regulatory module of the gene GaKNL1 was found to regulate the second cell wall through repressing the activity of REVOLUTA, and a tissue-selective module of GaJAZ1a was examined in response to water stress. Moreover, comparative genomics analysis of the JAZ1-related regulatory module revealed high conservation across plant species. In addition, 1155 functional modules were identified through integrating the co-expression network, module classification and function enrichment tools, which cover functions such as metabolism, stress responses, and transcriptional regulation. In the end, an online platform was built for network analysis (http://structuralbiology.cau.edu.cn/arboreum), which could help to refine the annotation of cotton gene function and establish a data mining system to identify functional genes or modules with important agronomic traits.
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