Gates are created by clicking into the plots. To create a rectangular gate, click once on the upper left corner, and close the gate by a double click in the lower right corner. For a polygonal gate, click on as many points as you wish and close the gate by double-clicking. To modify an existing gate, type the name of the gate you want to replace and draw it anew.
To store a state, click the button and remember the stateID that will be created
To restore a state, paste an exisiting stateID into the field below and click the button of your choice. Some useful predefined states:
Contains all gates used in transcriptomics analysis, as well as the populations from the hierarchical clustering. Displays plots for individual 1.
This module performs gene ontology analysis of the genes with the 10% highest/lowest loadings. It may take a moment for the results to appear.
To create a gene list, select the number of genes to store and the principle component to use
This is an interface to the MAST package described by Finak et al (
) which allows you to identify genes with differenial expression among arbitrary cell populations.
Computations take between one and 10 minutes depending on the number of cells to be analyzed.
Changing these values changes the display, without re-running the analysis.
You can create a gene list from all genes that are displayed as significant in the plot. Gene lists can be further analyzed in the Gene lists panelYou can perform a Gene Ontology enrichment on the genes that are displayed as significant.