Gene feature distribution: Modification sites distribution on different gene features, including Promoter, 5'UTR (UTR5), Start codon, CDS, 3'UTR (UTR3), Stop codon, Intron and Intergenic region. Y-axis denotes the frequency of sites (number of sites) while x-axis represents different gene features.
Gene types distribution: Modification sites distribution on different gene biotypes, such as protein coding gene, lncRNA, pseudogenes, rRNA, and miRNA. Y-axis indicates the frequency of sites (number of sites) while x-axis represents different gene biotypes.
Coverage plots for different features: Coverage plot for modification sites overlapping with different mRNA features. X-axis represents the bins (5' → 3' direction) while Y-axis indicates the mean coverage.
Boundary coverage for transcription start/end sites: Coverage plot for modification sites around transcription start sites and translation end sites. X-axis represents the nucleotide location around the site (5' → 3' direction) while Y-axis is the mean depth of coverage.
Boundary coverage for translation start/end sites: Coverage plot for modification sites around translation start sites (TSS) and translation end sites (TES). X-axis represents the nucleotide location around the site (5' → 3' direction) while Y-axis is the mean depth of coverage.
Boundary coverage for splice sites: Coverage plot for modification sites around 5' splice sites and 3' splice sites. For the coverage analysis around splice sites, the number of sites in each location is counted. X-axis represents the nucleotide location around the splice site (5' → 3' direction) while Y-axis indicates the mean depth of coverage.
RNA characteristics of genes with modifications: mRNA characteristics statistics between genes with modifications and other background genes. Y-axis in three plots (from left to right) represents length, GC content and minimum free energy (MFE), respectively. Modified genes Background genes
mRNA metagene plot: The rectangles in green, yellow and blue represent 5'UTR, CDS and 3'UTR, respectively. Y-axis denotes the density distribution of coverages.
Enriched motifs: Enriched motifs detect by Homer for the modification sites. The seqLogo plots for enriched motifs (top 5 as default) are showed.
(pvalue: 1e-34)
(pvalue: 1e-26)
(pvalue: 1e-24)
(pvalue: 1e-20)
(pvalue: 1e-19)
(pvalue: 1e-19)
(pvalue: 1e-19)
(pvalue: 1e-19)
(pvalue: 1e-18)
(pvalue: 1e-16)
(pvalue: 1e-16)
(pvalue: 1e-15)
(pvalue: 1e-15)
(pvalue: 1e-14)
(pvalue: 1e-13)
(pvalue: 1e-11)
(pvalue: 1e-9)
(pvalue: 1e-9)
Heatmap near transcription start and end sites: Heatmap of modification sites around transcription start sites and transcription end sites (genomic regions). X-axis represents the nucleotide position around the site (5' → 3' direction) while Y-axis represents all modified genes which is sorted by the number of modifications in each gene.
Heatmap near translation start and end sites: Heatmap of modification sites among translation start sites and translation end sites (transcriptic regions). X-axis represents the nucleotide position around the site (5' → 3' direction) while Y-axis represents all modified genes which is sorted by the number of modifications in each gene.
Gene Ontology functional enrichment for modified genes: Top 12 enriched terms are show in the bar plots. Y-axis in the bar plot indicates number of genes in according GO term.
Gene Ontology enriched terms
| ID | Description | GeneRatio | BgRatio | p.value | p.adjust | GO |
|---|
Functional Pathway enrichment for modified genes: Functional pathway enrichments for genes with modifications, which include KEGG for all 20 species, Top 12 enriched pathways are show in the barplots. Y-axis in the barplot indicates number of genes in according pathway category.
Enriched pathways
| ID | Description | Link | GeneRatio | BgRatio | p.value | p.adjust | Pathway_type |
|---|
| Transcript_id | Symbol | Jbrowse | Gene type | Promoter | 5UTR | CDS | 3UTR | StopCodon | Intron | Transcript |
|---|
| Chr | Start | End | Width | Gene type | Gene symbol | Jbrowse | Location | Transcript ID |
|---|