Helps and tips for using NanoMiner

To help new users to get a quick start on using NanoMiner, we provide several examples, and by following these examples, users will get a basic understanding how this system works, and how they can use it for their own research interests.


FAQ

We will update frequently asked questions under this section as we are receiving them from our users.


Select Topic



EXPRESSION PROFILE


Gene Search is used to check how gene expression of the queried gene(s) changes between samples within a set.

Click "Gene Search" from the left-hand side bar, and enter a gene/genes. For example:
PPBP, CXCL6, IL1B, CRTAM, TLR7, TLR5

↑ Back to Top ↑


Check the found gene(s), and select which of them will be included and shown in the expression plot.

↑ Back to Top ↑


Select a data set and click on "expression" to see the expression profile of the selected gene(s). Or, you can click on "boxplot" to check individual gene's boxplot within a dataset.

↑ Back to Top ↑


On this result page, you can find the gene expression plot(s) on the lower part (click the plot to get a larger version), and you can use the download link to get the full result table.

↑ Back to Top ↑


On boxplot result page, you can re-plot the figure by changing the grouping methods in the drop-down list, and "Update boxplot". Full result is downloadable from the same page.

↑ Back to Top ↑

DIFFERENTIAL EXPRESSION


DIFFERENTIAL EXPRESSION can be used to identify significant gene expression changes between co-normalised samples. In NanoMiner, we have pre-computed the differentially expressed genes (DEGs) in the nanoparticle studies we collected, so user can easily check whether or not a gene, or a group of genes are differentially expressed under any comparison in the NanoMiner.

Click "Differential Expression" from the left-hand side bar, and select the option "b. Search gene(s) from the comparison lists".

↑ Back to Top ↑


Enter a gene or a list of genes of your interest. In this example, we try to find a group of genes that are involved in GO term "immune reponse".

↑ Back to Top ↑


Select one or more found terms and make a group of genes.

↑ Back to Top ↑


Select one or more comparisons. Here we select all of the available comparisons in the NanoMiner.

↑ Back to Top ↑


In the result page, adjust P-value is the default value, you can see other values by using the drop-down list, and click "Update table". Below the drop-down list is the table which contains all the annotation information for those selected comparisons from the previous step. Under the annotation table, it is the full result of the differential expression for the given gene lists under different comparisons. Mouse over each "Comparison Type", a simplified annotation will be shown (highlighted in green color). The link to download the full DEGs result table is at the bottom of this page. For the users who want to briefly check how their searched genes behave under the comparisons, they can use "Full view" button.

↑ Back to Top ↑


Under full view, you can quickly spot the given gene(s) are mostly differentially expressed in which comparison(s). For example, in this case, comparisons "PBMCs_AuNP_24hr_vs_PBMCs_Control" and "PBMCs_AuNP_48hr_vs_PBMCs_Control" seem have many DEGs (or RED) shown in this table.

↑ Back to Top ↑