ImmiR: a database of miRNAs associated with immune checkpoints and immune infiltration.
Methods & tools
miRNA-target interactions
The miRNA-target interactions in ImmiR are categorized into three types: "Validated," "Predicted," and "Without any evidence."
The "Validated" interactions are sourced from the miRTarBase database Release 6.1, which includes over 366,000 interactions.
Predicted miRNA targets are identified by using 12 miRNA target prediction tools, including DIANA-microT, MicroT4, miRBridge, miRDB, miRMap, PITA, RNAhybrid, TargetScan, PICTAR2, RNA22, miRWalk, and miRanda.
Only targets identified by at least 6 tools are retained to enhance the reliability of the prediction results.
Reference of tools utilized in ImmiR
The below table provides the PMID of the tools we used in the Immune infiltration association section. You can use the PMID of each tool to search for more detailed information.
Tools
PMID
CIBERSORT
PMID: 25822800
XCELL
PMID: 29141660
TIMER
PMID: 32442275
MCP-counter
PMID: 27765066
EPIC
PMID: 29130882
QuanTIseq
PMID: 31126321
ImmuCellAI
PMID: 32274301
ESTIMATE
PMID: 24113773
TIDE
PMID: 30127393
Plot interpretation - correlation plot
In each heatmap and table of ImmiR, you can view the correlation of two variables by clicking on specific cells or rows. By doing so, correlation plots related to your selection will pop up. If the "Purity Adjustment" option has been chosen in the input data process, you will see two correlation plots.
To illustrate the correlation plots, consider the example of hsa-miR-1306-3p and T cells CD4 memory XCELL in BRCA under the miRNA section in the Immune infiltration association as below.
The details of the two plots will be presented in the order indicated in the screenshot.
The plot on the right displays the correlation between selected immune infiltrates and log2 expression of miRNA. This plot examines whether the miRNA impacts specific immune infiltrates. By performing tumor purity correction, the influences of tumor purity can be eliminated.
The plot on the left illustrates the correlation between tumor purity and log2 miRNA expression. This plot primarily focuses on determining whether the source of the miRNA is from the tumor (positive correlation) or the surrounding stroma cells (negative correlation).
Manipulation of figures & tables
Figure manipulation
As the mouse hovers over the interactive figure, the toolbar appears at the top of each figure.
Download figure. Press to download the figure as a png.
Zoom. Press to circle the area that you want to zoom in.
Zoom in. Press to zoom in the figure.
Zoom out. Press to zoom out the figure.
Reset axes. Press to back to the original setting of the figure.
Table manipulation
The toolbar is on the top of each table.
Download. Press the “CSV” button on the top-left of the table to download the table as a CSV file.
Copy. Press the “Copy” button next to the “CSV” button on the top-left of the table to copy the whole table to the clipboard.
Search. Enter keywords on the top-right of the table to get a quick search over the table.
