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<Control Group> vs <Comparison Group> Report

This report lists the results for the differential expression analysis.

Differential Expression

Statistic

Description

Annotation Gene Count

Number of genes in the annotation.

Assessed Gene Count

Number of genes tested for statistical significance.

ΔGene Count

Number of significant differentially expressed genes.

Merged Gene Counts

Link to the merged gene count file.

DESeq2 Results

Link to the DESeq2 result file.

Differential Expression Heatmap

The Differential Expression Heat Map shows the level of expression of genes across various comparable samples. The heat map shows only the on-target genes if you selected a panel.

The gene dendrogram shows the clustering of genes and the correlation between two gene clusters.

The expressed genes are assigned to different colors.

• Red—Genes with low expression.
• Black—Genes with average expression.
• Neon green—Genes with high expression.

To specify a gene, expand the Jump to Gene drop-down list, and then select the gene.

To specify a sample, expand the Jump to Sample drop-down list, and then select the sample.

To save the plot as scalable vector graphics (SVG), select Save Plot as SVG.

To export data from plot as TeamViewer Session, select Export Heatmap Data (TSV).

Gene Browser

The Gene Browser shows an interactive scatter plot of the log2 (FPKM) counts of genes for the control samples and comparison samples groups.

To display genes that have a specific value (or range of values), modify the following filters:

• q Value–Drag the control handles on the slider to change the lower and upper limits.
• | log2(Fold Change) |–Drag the control handles on the slider to change the lower and upper limits.
• log2(<Control> Count)–Drag the control handles on the slider to change the lower and upper limits.
• log2(<Comparison> Count)–Drag the control handles on the slider to change the lower and upper limits.
• Significant–Expand the Significant drop-down list and select a significant value.
• Status–Expand the Status drop-down list and select a status value.
• Gene–Enter a gene name.

To save the plot as scalable vector graphics (SVG), select Save Plot as SVG.

The table shows only the on-target genes if you selected a panel.

Statistic

Description

Gene

Gene symbol

Status
• Low–Mean expression across all samples is too low to assess statistical significance of differential expression.
• OK–Statistical test for significant differential expression was performed.

log2(<sample group> Count)

Average expression in each group. Calculated from Mean Count and log2(Fold Change).

Mean Count

Normalized mean count of the control and comparison groups.

log2(Fold Change)

log2 of fold change of comparison over control groups

Std. Err. log2(Fold Change)

Standard error of the log2(Fold Change) estimate.

q Value

Multiple testing adjusted p-value of differential expression. This value is filtering significance differential expression.

Significant
• True–q Value is less than the false discovery rate threshold.
• False–q Value is higher than or equal to the false discovery rate.

The default false discovery rate threshold is 0.05.

To save the table as a CSV file, select Save Filtered Table.