Search by gene

In Gene View,scRNASeqDB provides general information, gene expression, summary of gene expression in each cell group of a dataset, as well as correlated genes.

By selecting By Gene menu item, users can search the specific gene expression by inputing the gene symbol or Ensembl ID (Figure 3). Alternatively, user can select a gene from Gene Cloud directly for gene view.

Figure 3. Search by gene interface.

In figure 4, users can see the query result for TBK1. By clicking the link below the gene name of "TBK1", user can visit gene expression of TBK1 in the specific dataset.

Figure 4. The search result for TBK1.

In Gene View page (Figure 5), the general information of TBK1 is provided, including gene name, synonyms, Ensembl ID, description, chromosome location, external links. In Gene Expression section, TBK1 expression in each sample is displayed in heatmap, as well as minimum value, median value and maximum value in each cell group. The heatmap can be exported as a picture or a pdf document by clicking the button in the upper-right corner.

Figure 5. The Gene View of TBK1 is provided.

In addition, the boxplots in each cell group and FDR for gene differential expression between cell groups are provided (Figure 6). BPSC (Vu et al.Bioinformatics, 2016) was used to obtain the differential expression genes. NS represents there are no significant difference for TBK1 between two cell groups.

Figure 6. Gene expression in each group for TBK1.

From Figure 7 and 8, top 100 positive and negative correlated genes can be obtained for the specific gene (e.g. TBK1). In addition, the correlated genes can be used to explore their functions by using DAVID. When users click on the button KEGG, GO, or Others, the correlated genes will be annotated using DAVID annotation system. These genes can be obtained by clicking the Gene List button.

Figure 7. The correlated genes for the specific gene are provided. Additionally, GO and pathway annotations are also provided.

Figure 8. Top 100 positive and negative correlated genes for TBK1 in dataset GSE36552 is provided.