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1. Query

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Our visualization tool allows you to explore the functional gene interactions within each tissue. On the 'Home' page, you may select a tissue or a cell type and input the gene name of your interest, and the gene-level network will be displayed. Below, we use APOE in the brain network as an example to illustrate how to explore our interactive website.

Step 1: Select a tissue or a cell type.

Step 2: Input a gene symbol.

Step 3: Click the "Search" button, and you will be guided to a page showing networks and associated analysis.

2. Result overview

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After your query a gene in a specific tissue, you will be guided to the result page for network visualization as well as multiple analysis, including gene ontology enrichment analysis (GOEA), disease/traits enrichment, genetically associated diseases/traits, and available drugs targeting the gene.

Note 1: If the gene exist in the queried tissue network, it will return the gene information and gene pair number of its local network (including between-neighbor interactions), which contains the gene and its top 25 neighbors.

Note 2: To download the local network of your queried gene, click the 'Download gene network data' button.

Note 3: The color code indicates the type of genes.

Note 4: The sliding bar determines the threshold above which the edges with their neighbors will be shown.

Note 5: Analysis results of the local network. The default content is co-functional probability for the top connected 25 genes.

3. Analysis

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Note 6: We used GoTermFinder to perform GO enrichment analysis.

Note 7: We used the "Curated gene-disease associations" downloaded from the DisGeNET database (version 5.0) for disease enrichment analysis.

Note 8: Associated disease/traits for the queried gene based on GWAS Catalog(2020-11-20).

Note 9: Associated drugs targeting the queried gene based on DGIdb (2021-May).