Oryza sativa co-expression module genes

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Note: when large module is loaded or too many connections are chosen, the network visualization may takes several minutes to show. Citation: Planta 249 (5), 1487-1501 

            

            

              

                

                
Table 1. The top correlated genes (PCC > 0.6)

                
                
Functional enrichment for top 30 correlated genes

                

                
Table 2. The top connected neighbor genes

                

                

              

            

            







        
  

Genelist

    
 	
    Genelist tab provides the following information about the query module: Entrez gene ID, kTotal: total connectivity, kWithin: within module connectivity, kOut: out of module connectivity, kDiff: the difference between within module connectivity and out of module connectivity, Module: the numbering of module.
     
 	  	



Hub genes

    
 	
    Hub genes provides information for top 3 connected intramodule genes
    
 	



Annotations

    
 	
    It provides information about the selected module, including GO and pathway enrichment.
    
 	



Network

    
 	
    To visualize a network module, users can select a module in the left panel. To control the network size, users can slide the percentage bar to show only the top connected connections. Users can pull and drag the element in the network.
    
 	




Gene function investigation

    
 	
    We may be interested in a specific gene in the module. How is the gene correlated with all other genes? What is the gene functional anntations of those highly correlated genes? Which gene is the closest neighbor? Answering these questions may help to provide some clue for the gene we are interested. In the left panel "Input a query gene for function investigation" box, users can provide an MSU, RAP-db or NCBI EntrezID to explore its function by gene correlation analysis.
    
 	




Helps

    
 	
    Helps tab provides a simple document for how to use the web tool.
    
 	
















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