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Currently, we only support HGNC official IDs for genes. We provide a ID mapper function to map other gene names/synonyms to HGNC IDs.

Network Query

[example]
Please paste the terms you want to query!

If you do not know which GO terms you are interested in, you can still specify the number of GO terms to include in the p-value matrix, or just use all the GO terms in the database (Note, to use all GO terms are not recommended because the computation will be very slow). Try an example.

GO Terms[example]

Please enter your lists of genes in the following boxes to construct a gene-gene network. Currently, we support identifying genes by their unique HGNC ID. To map gene symbols to their corresponding HGNC IDs, you can use our ID mapper.

Try an example. The example genes are from pathways associated with Systemic Lupus Erythematosus (SLE). Specifically, they correspond to the following genes:

interferon regulatory factor 7(IRF7)
TNF alpha induced protein 3(TNFAIP3)
Fc fragment of IgG receptor IIb(FCGR2B)
interferon regulatory factor 5(IRF5)
Fc fragment of IgG receptor IIa(FCGR2A)
Fc fragment of IgG receptor IIIb(FCGR3B)
interferon induced with helicase C domain 1(IFIH1)
integrin subunit alpha M(ITGAM)
solute carrier family 15 member 4(SLC15A4)
tyrosine kinase 2(TYK2)
Fc fragment of IgG receptor IIIa(FCGR3A)
toll like receptor 7(TLR7)
microRNA 146a(MIR146A)
TNFAIP3 interacting protein 1(TNIP1)
signal transducer and activator of transcription 4(STAT4)
interferon regulatory factor 8(IRF8)
ubiquitin conjugating enzyme E2 L3(UBE2L3)
Optional GO terms

You can include GO terms in the network query. If so, a p-value matrix between queried genes and GO terms is calculated. You can further use this matrix in bayesGO. See Software page for details.

Use GO terms

If you do not know which GO terms you are interested in, you can still specify the number of GO terms to include in the p-value matrix, or just use all the GO terms in the database (Note, to use all GO terms are not recommended because the computation will be very slow).

View Matrix

You can view the resulting cosine similarity matrix between genes and genes by clicking on the 'View' button and choose 'Network Matrix'. If additional GO terms are queried, you can also view the hypergeometric p-value matrix between genes and GO terms.

Download Graph and Matrix

You can download the resulting netwrok graph as well as the cosine similarity matrix between genes and genes by clicking on the 'Download' button and choose corresponding options. If additional GO terms are queried, you can also download the hypergeometric p-value matrix between genes and GO terms. The downloaded graph is '.png' format and the downloaded matrix is '.csv' format.

Community Detection

We provide a function called 'Community Detection' to detect the cluster in the gene-gene network. You can perform the community detection by clicking on the 'Community Detection' button.

A tab in the 'Network Analysis' section will show up when the detection finishes. You can change the color of the cluster or check the averaged p-value between each GO term and the cluster of genes.

Global GO Analysis

'Global GO Analysis' calculates the averaged p-value of a given gene with all GO terms.

Network Customization

You can customize the network by changing the options under the 'Customize the Network' tab.

The details of all customizations are listed below:

Customizations Description
Edge Display We provide two methods to display the network. You can choose 'Cosine Similarity' method, which constructs the network based on computed cosine similarity scores. You can specify the cut-off value for cosine similarity. Two genes are connected if their similarity score is above the cut-off. In the other method, you can choose the maximum number of associations(edges) allowed for each gene. The associations are picked For example, the default value of 2 restricts each gene to have 2 associations with other genes at maximum.
Find a Gene You can search for a specific gene in the input box. The camera will zoom in if you select a specific gene.
Network Layout You can update the network layout by changing the distance between each nodes. This is useful when you have performed the community detection. Genes within a gene cluster will locate near each other. Also, you can restore the original network by clicking on 'Zoom Back'.
Network Info

You can find information about genes and gene-gene associations when you click on a node or an edge. When you click on a gene node, name and symbol for the specific gene will display. In addition, you can go to GeneCard to find more information about the gene by clicking on 'Link to GeneCard'

When you click on a gene-gene association, symbols of two gene nodes and the cosine similarity between two genes will display. You can also compare the two genes by clicking on 'Compare Nodes'. This will direct you to a table that lists hypergeometric p-values between these two genes and all GO terms. You can download the corresponding matrix of the comparison.

Data Table

You can find cosine similarity between each pair of two genes in the data table tab. Note, the data is the same as that in the cosine similarity matrix. We only change the format to display the data so that you can order by gene name or the similarity scores.

Community Detection

We provide a function called 'Community Detection' to detect the cluster in the gene-gene network. You can perform the community detection by clicking on the 'Community Detection' button.

A tab in the 'Network Analysis' section will show up when the detection finishes. You can change the color of the cluster or check the averaged p-value between each GO term and the cluster of genes.

Global GO Analysis

'Global GO Analysis' calculates the averaged p-value of a given gene with all GO terms.

Search Again

You can return to the search page and start over by clicking on 'Search Again'.

Check Documentation

If you forget the above information when you head to the results page. Do not worry, you can still check documentation by clicking on the book icon.