deepAnno conducts in-depth analysis of data uploaded by users. It firstly identifies RNA modification sites if peaks file was uploaded and skip this step if sites file was uploaded. Then annotates these RNA modification sites and presents their distribution on different gene biotypes like protein coding genes, circRNAs, lncRNAs, rRNAs, tRNAs and so on, and gene features containing 5'UTR, 3'UTR, exon, intron and CDS. It futhermore presents the possible formation mechanism of RNA modification sites, guided by snoRNAs and/or enzymes like methylases, that based on mechnism analysis of our database. deepAnno also provides users the distribution of RNA modifications identified by it on mRNA features including CDS, 5'UTR and 3'UTR. In addition, it also presents coverage plot of RNA modifications around transcription start/end sites, translation start/end sites and 5'/3' splicing sites.

modFunction predicts biological roles of RNA modifications by a series of functional analysis. It identifies and annotates the RNA modification sites from uploaded data and presents their relationships with RBPs, miRNA targets, SNPs and SNVs. It presents RBPs and miRNAs that their binding sites contain RNA modifications to facilitate users to study the mechanisms and biological roles of RNA modifications. In addition, modFunction performs GO enrichment analysis, functional annotation clustering and KEGG pathway mapping after annotating RNA modifications.

modGeneTool present all RNA modification sites stored in our database of each gene or transcript uploaded by user. The results show the details of RNA modifications including types, number, seq-types, cell/tissue types and so on.

modMetagene presents a metagene plot of the RNA modifications along a transcript model from uploaded data, like uploaded files or pasted text. It shows the density of RNA modification sites on different regions (5'UTR, 3'UTR and CDS) of the transcript.

modAnnotation identifies RNA modification sites form uploaded data and annotates these sites that were based on all of the RNA modification sites recorded in our database. These results show the origin of RNA modification sites, such as genes, transcripts and regions, as well as indicate the cell/tissue types and datasets of each RNA modification sites, which were based on analysis of a vast amount of data.

Conserved Site module was used to analyze conserved RNA modification sites in different species. The results list all sites of different species stored in our database that are conservatiove to the RNA modification sites uploaded by users or identified from uploaded peaks.

Histone.