Figure 1. Gene expression profiling of land and water form ofRiccia fluitans based on direct RNA
A. Dotplot chart of enrichment ontology of genes. The circles
represent pathways described along the y-axis, colors reflect the
adjusted p-value of enrichment statistics, and the sizes of the circles
represent the number of genes enriched in each pathway.
B. The dotplot illustrates the correlations between
statistically significant genes from nanopore sequencing and transcripts
from Illumina sequencing. The x-axis represents log2FoldChange values
for nanopore sequencing, while the y-axis depicts log2FoldChange values
for Illumina sequencing. The red line highlights the Pearson
correlations. The R value is displayed in the upper left corner.
C. Circular plot depicting the relationships between
significant genes. The first track shows 3 heatmaps, which show the
expression level in each of the significant genes. The green-black-red
scale represents the expression of DEGs, the blue-black-red scale
represents the expression of DELs, and the green-black-yellow scale
represents the expression of other RNAs. The second track describes the
log2FoldChange values of upregulated (red) and downregulated (blue)
genes. The third track shows the unique genes that were found in the
nanopore data analysis (purple color) as well as the common genes (gold
color) to the differential analysis in Illumina and Nanopore. The
internal track depicts the correlation relationships, where the blue
link represents the correlations between DEGs and DELs, green for DEGs
and other RNAs, and orange for DELs and other RNA.
D. The MA plot visualizes the association between
log2FoldChange and log2 from the average of normalized counts. The
x-axis displays the log2 of the average of the normalized gene counts,
while the y-axis illustrates the log2FoldChange for the gene. Squares
represent irrelevant transcripts, triangles represent upregulated
transcripts, circles represent downregulated transcripts, and the green
color indicates DELs, red indicates DEGs, blue indicates other RNAs, and
grey indicates no significant genes.
E. Volcano plot depicting log2 Fold Change (log2FC) for
significant genes. The x-axis displays the log2FC values for each gene,
while the y-axis shows the negative log-adjusted p-value (p-adjusted).
The horizontal dashed line represents the negative logarithmic
p-adjusted cutoff value (0.05), and the two vertical lines equal the
absolute value of 1 log2FC. Coloured points indicate statistically
significant genes, while grey points represent non-significant genes.