Our ccnWheat database for four species, namely Triticum aestivum (AABBDD), Triticum dicoccoides (AABB), Triticum urartu (AA), Aegilops tauschii (DD). Below is the detail information for using our ccnWheat database.
Using Quick search in the navigation, you can submit one gene of you interested, then the detail information about this gene would be displayed in our result page.
(1) Network search (click here)
Network search support searching of a single gene or a list of genes, we also provide one-click search for the homologous genes of the gene and its related networks in the result page.
(2) Network comparison (click here)
Network comparison suopport global and conditional (tissue-specific or stress-treatment) network search of Triticum aestivum (AABBDD), and also support two species comparison.
(3) Ortholog network search (click here)
Ortholog network search provide ortholog pairs for three species, you can choose the gene among them to compare.
(4) How to use the local version of cytoscape to draw the network (click here)
First, you can adjust the nodes and edges of network as you like, then choose the PNG or JPG formats, and click the "export" button to download the picture.
If you want more better graphics and the other formats, you can click the link of "Network gene list download", then download the gene list. You only need columns 1, 2, and 5 to import the local version of Cytoscape. Then please see Cytoscape manual for help.
(5) For all types of network search (click here)
We provide the results (nodes, edges) and the analysis tools (GO, GSEA, motif, expression profiling) of one-click network search in the result detail page.
A list of genes are required here for functional modules enrichment, according to statistical test method and multi-test adjustment method, significant enrichment dunctional modules will be listed, together with annotation, links of functional module detail.
(1) For Functional annotaion (click here)
We provide different types of annotation data, you can browser our Function annotation navigation, and choose the type of data you interested, and all genes in this type will be displayed.
(2) For tools (click here)
(A) We provide analysis tools and basic tools for users to use.
(B) Basic tools include Sequence extraction, FPKM extraction, ID conversion, Blast etc., and we use Sequence extraction for example, you can put a gene list or genomic location to get the sequence.
(C) Analysis tools include GSEA analysis, GO analysis, motif analysis, and module analisis. And we use GSEA analysis for example, you can put a gene list and choose the gene sets you want to analysis.
Zhen Su's Lab introduction:http://bioinformatics.cau.edu.cn/ZhenSuLab/. For any questions, comments or suggestions about our website, please contact us: lzq2688@cau.edu.cn , and zhensu@cau.edu.cn.
