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A new data node named ‘Single cell counts’ will be displayed in Flow if the task is running (Figure 6).  To open the task report, simply double click the output data node, or select the ‘Task report’ in the section after clicking the data node after the tasking running is finished. User then will find the task report (Figure 7) is the same to the ‘Summary HTML’ from Cell Ranger output.

We recommend filtering to a set of genes you want to test for enrichment, but Gene set enrichment will run on any Feature list data node. 

• Click a Feature list data node
• Click the Biological interpretation section of the toolbox
• Click Gene set enrichment 
• Configure the background gene list (optional)

The background gene list is used as the list of possible genes. By default, this is the genes included in the selected gene set database. If your assay limits the genes that could be detected, you may want to specify a background list.

• Choose the Gene set 

The gene sets available for the current Assembly are listed under the Gene set drop-down list. The assembly is automatically selected, if possible. If the assembly cannot be detected, you can specify it using a drop-down menu.

• Click Finish to run (Figure 1)

By default, the groups are defined by Gene Ontology (GO), a bioinformatics initiative to unify the representation of gene and gene product attributes across various species [1, 2].

Alternatively, selecting the Add gene ontology source from the Gene set drop down list option opens another dialog (Figure 3), where you can either Download gene set from Partek^® (Recent GO database gene sets for human, mouse and rat are available) or Import gene set. The latter option takes you to the file browser, where you can point to the file that you want to use (not shown). Partek^® Flow^® accepts .gmt files as gene set inputs.

The result is stored under an Enrichment task node. To open it, double click on the node or select the respective Task report from the context sensitive menu.

Cell ranger task report

Figure 4 shows an example Gene set enrichment task report. The table contains one gene set per row (Gene set column; the column entries are hyperlinks when using the distributed GO gene sets), with the category name in the Description column. The categories are ranked by the Enrichment score, which is the negative natural logarithm of the enrichment p-value (P-value column) derived from Fisher's exact test on the underlying contingency table. The higher the enrichment score, the more overrepresented the GO category is within the input list of significant genes. The columns can be searched by typing in the search term in the respective box (and hitting Enter), or sorted by selecting the double arrow icon ( Image Removed ).

The contingency table (Figure 5) can be displayed by selecting the View gene breakdown chart icon on the right (Image Removed). The term "list" refers to the list of significant genes, while the term "set" refers to the respective GO category. The first row of the contingency table is also seen in the report, namely the Genes in list and Genes not in list columns.

The View extra details (Image Removed) button provides additional information on the GO category (Figure 6). In addition to the details already given in the report, a full list of Genes in list and Genes not in list can be inspected and downloaded (Download data) to the local computer as a text file.

As previously mentioned, if you are using the GO gene sets distributed by Partek, the GO identifiers in the first column are hyperlinks to the Gene Ontology web-site entries (an example shown in Figure 7).

References

1. https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome

2. https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/6.0/release-notes

3. https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/4.0/release-notes

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