Project: NEGEDIA
This report summarises differential gene expression analysis as performed by the negedia/degsanalysis pipeline.
A summary of samples sequencing metrics is below:
Comparisons defined by the user are listed in the following table:
Results
Counts
The results are derived from the global gene expression analysis of the experiment, focusing exclusively on genes that are expressed at least in one sample (genes with 0 counts in all the samples are excluded).
Preliminary analysis
Expression value distributions
The following plots show the log2 expression value distributions of the experiment samples.
The distribution of normalised counts per gene, for each sample, is represented in the form of a box plot.
The density plot represents the distribution of the log2 normalised counts.
Samples correlation
Principal components analysis was conducted based on the 500 most variable genes. Each component was annotated with its percent contribution to variance.
Normalised (Condition)
ANOVA test was used to determine assocations between continuous principal components and categorical covariates (including the variable of interest).
The resulting p values are illustrated below.
The variable ‘Condition’ shows an association with PC1 (49.7%) (p = 0.00).
A hierarchical clustering of genes was undertaken based on the top 500 most variable genes. Distances between genes were estimated based on spearman correlation.
Normalised (Condition)
Differential analysis
Differential expressed genes
Differential expression details
The red dots represent Differentially Expressed Genes (DEGs). Genes with a log2 fold change greater than or equal to the specified value are upregulated compared to the reference (dots on the right). Genes with a log2 fold change smaller than or equal to the specified value are downregulated compared to the reference (dots on the left). Genes with an FDR or padj value less than or equal to 0.05 are considered statistically significant.
Heatmap of normalized scaled expression per replicate of DEGs in the selected comparison.
The red dots represent Differentially Expressed Genes (DEGs). Genes with a log2 fold change greater than or equal to the specified value are upregulated compared to the reference (dots on the right). Genes with a log2 fold change smaller than or equal to the specified value are downregulated compared to the reference (dots on the left). Genes with an FDR or padj value less than or equal to 0.05 are considered statistically significant.
Heatmap of normalized scaled expression per replicate of DEGs in the selected comparison.