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Database Commons - ccNET

ccNET

Citations: 0

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Short name ccNET
Full name
Description an online database for comparative gene functional analyses at a multi-dimensional network and epigenomic level across diploid and polyploid Gossypium species
URL http://structuralbiology.cau.edu.cn/gossypium
Year founded 2014
Last update & version 2016-12-22    
Availability Free to all users
University/Institution hosted China Agricultural University
Address State key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences
City Beijing
Province/State
Country/Region China
Contact name Zhen Su
Contact email zhensu@cau.edu.cn
Data type(s)
Major organism(s)
Keyword(s)
  • co-expression network
  • miRNA-target network
  • protein-protein interaction (PPI)
Publication(s)
  • ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium. [PMID: 28053168]

    Qi You, Wenying Xu, Kang Zhang, Liwei Zhang, Xin Yi, Dongxia Yao, Chunchao Wang, Xueyan Zhang, Xinhua Zhao, Nicholas J Provart, Fuguang Li, Zhen Su
    Nucleic acids research 2017:45(D1)
    0 Citations (Google Scholar as of 2017-02-20)

    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. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Accessibility

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HTTP status codeDate requested
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200 OK2017-09-26
200 OK2017-09-22
200 OK2017-09-19
200 OK2017-09-15
200 OK2017-09-12
200 OK2017-09-08
200 OK2017-09-05
200 OK2017-09-01
200 OK2017-08-29
200 OK2017-08-25
200 OK2017-08-22
200 OK2017-08-18
200 OK2017-08-15
200 OK2017-08-11
200 OK2017-08-08
200 OK2017-08-04
200 OK2017-08-01
200 OK2017-07-28
200 OK2017-07-25
200 OK2017-07-21
200 OK2017-07-18
200 OK2017-07-14
200 OK2017-07-04
200 OK2017-06-30
200 OK2017-06-27
200 OK2017-06-23
200 OK2017-06-20
200 OK2017-06-16
200 OK2017-06-13
200 OK2017-06-09
200 OK2017-06-06
200 OK2017-06-02
200 OK2017-05-30
-1 Failed2017-05-26
-1 Failed2017-05-23
200 OK2017-05-19
200 OK2017-05-16
200 OK2017-05-12
-1 Failed2017-05-09
200 OK2017-05-05
200 OK2017-05-02
200 OK2017-04-28
200 OK2017-04-25
200 OK2017-04-21
200 OK2017-04-18
200 OK2017-04-14
200 OK2017-04-11
200 OK2017-04-07
200 OK2017-04-04
200 OK2017-03-31
200 OK2017-03-28
200 OK2017-03-24
200 OK2017-03-21
200 OK2017-03-17
200 OK2017-03-14
200 OK2017-03-10
200 OK2017-03-07
200 OK2017-03-03
200 OK2017-02-28
200 OK2017-02-24
200 OK2017-02-21

Tags

Expression Interaction and Network Modification
Gossypium
co-expression network miRNA-target network protein-protein interaction (PPI)

Record metadata

  • Created on: 2017-02-20
  • Curated by:
    • Lina Ma [2017-06-14]
    • Shixiang Sun [2017-02-20]
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