Zebrafish module genes

Module
Genelist
Note: when large module is loaded or too many connections are chosen, the network visualization may takes several minutes to show.

Sample information download url 


            

            

              

                

                  
                  
                

                

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

                
                
Functional enrichment for top 30 correlated genes

                

                
Table 2. The top connected neighbor genes

                

                

              

            

            

              

                
                  

                
                

              

            

            

              

                

                  
                  

                    
                    
                  

                

                
Your input is:

                

                
The top 30 most similar experiments are:

                

              

            

            

              

                

                  
                  

                    
                    
                  

                

                
Your input is:

                

                
The pair-wise experiment similarities are:

                

                
Note: full list of conditions is available in the left panel

              

            

            







        
  
Network summary

    
 	
    Network summary tab provides the overall information for the all modules identified. Column 1 is the numbering of modules; column 2 is the gene number in that module; column 3 is the adjusted term enrichment P value; column 4 is term ID; column 5 is the type of ID in corresponding database; column 6 is the term name;42hp column 7 is the brief sample description for the sample with highest modulel gene expression.
     
 	  	



Genelist

    
 	
    Genelist tab provides the following information about the query module: Affymetrix ID, Entrez gene ID, Gene Symbol, 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 ID to explore its function by gene correlation analysis.
    
 	



Module signature

    
 	
    As the high dimensional microarray data have been reduced to only tens of co-expressed modules, people may be interested in if those modules are correlated with a specific condition. The module level expression is summarized by its first component by PCA analysis, which represents module gene expression. Higher value suggests higher expression of that module in a specific condition. The module may represent a signature for that condition. For example, in the left panel, module 51 is selected, the "Module signature" tab shows experiments with high M51 expression. The first one is sample from stage 4.3 hpf wildtype embryos. In the "Annotations" tab, you can check that M51 genes are annotated with mitotic.
    
 	



Finding similar experiments

    
 	
    Sometimes, people are interested in which condition most resambles to another experiment profile. Those similarity may indicate similar mechanisms under different condtitions. Therefore, users can provide a condtion in the "Select a condition" box. Then, the top 30 similar experiments are returned with detailed information.
    
 	



Compare experiments

    
 	
    The similarities between conditions are an interesting topic. For example, if you are interested in whether the gene expression patterns are more similar among biotic than that of abiotic conditions or not, you should care the correlations between those condition profiles. Thus, the Compare experiments tab provides such an analysis. You choose multiple condtions by selecting interesting experiments from the "Select conditions to compare" box, then sample information and condition similarity are returned. How is the similarity metric calculated? Each condition is represented by a vector of ME values, which are the expression of each module. Then a similarity matrix for pair-wise similarity between conditions are returned. For example, if you choose three conditions GSM1070393 (4 h retinoic acid treatment post fertilization embryo), GSM1070395 (6 h retinoic acid treatment post fertilization embryo) and GSM1070397 (9 h retinoic acid treatment post fertilization embryo), you will find that 6 h and 9 h treatment is more similar than 6 h and 4 h, which indicates 6 h may be a critical time point. If you choose another three datasets from the same experiment (GSM1008113, GSM1008114 and GSM1008115), you can find that these replicates are very similar with correlations all higher than 0.97
    
 	



Citation

    
 	
    Large-scale analysis of zebrafish (Danio rerio) transcriptomes identifies functional modules associated with phenotypes. Marine Genomics, April 2020, 100770.
    
 	


Helps

    
 	
    Helps tab provides a simple document for how to use the web tool. Please contact weilau@fafu.edu.cn if you have any idea or question about our site.
    
 	










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