Seurat -Find conserved cluster markers and DE genes in two samples
This tool gives you
for a given cluster. "Conditions" are the ones determined in the Setup tool with the Sample or group name parameter.
This tool can be used for two sample combined Seurat objects.
- The cell type markers that are conserved across conditions (conserved_markers.tsv) and
- The differentially expressed genes between the conditions (de-list.tsv)
As inputs, give the combined Seurat object.
Select the cluster you want to inspect by setting its name in the parameter field. As an example, the parameter is
set to cluster "3".
de-list.tsv is a table containing the differentially expressed genes for the chosen cluster, compared
to all the other cells in the data, and associated statistics:
- p-val = p-values for the differentially expressed genes (larger the p-value -> higher the
likelihood that the gene is in the list just be chance)
- avg_logFC = average log fold change (how much higher (lower) the expression of this gene is in the chosen
cluster, compared to all the other cells
- pct.1 = what percentage of the cells in the chosen cluster show some expression for this gene
- pct.2 = what percentage of the cells not in the chosen cluster (=all the other cells) show some expression for this gene
- p-val_adj = adjusted/corrected p-value. This value is multiple testing corrected:
when we test over thousands of genes, we would statistically start getting some significantly differentially
expressed genes just by chance. There are different methods to correct for this,
here a Bonferroni correction is used. When filtering the table and reporting your results,
use this value.
conserved_markers.tsv is a table containing a ranked list of conserved markers in the chosen cluster (=genes that show changes in
expression in this particular cell type/cluster, regardless of the treatment/sample),
and associated statistics:
- the values listed above for both samples in the data
- max_p-val = maximum p-value of the two samples (note: not looking at the adjusted p-values)
- min_p-val = minimum p-value of the two samples (note: not looking at the adjusted p-values)
For more details, please check the Seurat tutorials for multiple sample analysis.
- conserved_markers.tsv: Conserved cell type markers across the conditions
- de-list.tsv: Differentially expressed genes between the conditions