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Navigation1. RNA A-to-I editing information for 33 cancers2. Understanding annotation of CAeditome Search page, example: GRIA2 Gene search result page Gene annotation result page 1) Gene summary 2) RNA A-to-I events 3) RNA A-to-I editing positional annotations 4) RNA A-to-I editing events in the alternative splicing sites 5) Differntial gene expression between RNA A-to-I edited versus non-edited samples 6) Protein coding region RNA A-to-I editings 7) The effects of the RNA editing to the miRNA binding sites 8) The effects of the RNA editing to the stability of the RNA structures 9) Relation with ADAR 10) Relation with Cancer stages and survival state 11) Related drugs and diseases with this gene 3. Download data and contact us 1. Identifying RNA A-to-I editing events in 33 cancers We downloaded RNA-Seq bam files, SNP array data, gene expression values and clinical information of 11,056 samples across 33 cancer types from The Cancer Genome Atlas (TCGA). The alternative splicing landscape for these samples were collected from one recent study (Kahles et al. 2018). For all the samples across 33 cancer types, we firstly detected RNA editing events from individual RNA-seq bam files by the script of REDItoolKnown.py (REDItools) (17) with default setting (e.g., minimal read coverage, 10; minimal quality score, 30; and minimal mapping quality score, 255) and hg38 (GENCODE (v.22) reference files same to that used by the GDC data harmonization and generation pipelines. To ensure the confident identification of A-to-I RNA editing events, we focused on known editing sites from REDIportal (January 2021), removed possible SNP data, and filtered out the candidates with supporting reads under three or editing frequency less than 0.1. Eventually, we selected one kind of RNA editing events, A-to-I RNA editing for further analysis, because of its abundance in human. 2. Understanding CAeditome's annotation categories Search page, example: GRIA2 - Input query: Official HUGO gene symbol or Entrez gene ID.  Gene search result page Select your gene from the gene list.  Gene annotation result page These are CAeditome's annotation categories for your query with links to their corresponding annotation parts.  1) Gene summary category This category shows the information of the RNA edited gene. Firstly, it shows each partner gene's overall information from basic information such as symbol, alias, and locations and ENST accessions. This table also shows the tissue and cancer type information including manually curated PubMed article information.  2) 'RNA A-to-I editing events' category This category provides the detailed RNA editing event information including genomic location from the UCSC genome browser, distribution of editing frequency across 33 cancers, and differential RNA editing events in cancer not in normal tissue.  3) 'RNA A-to-I editing positional annotations' category This category provides the annotation by coding/repeatitive regions and gene structure related annotations.  4) 'RNA A-to-I editing events in the alternative splicing sites' category This category provides the RNA editing information located in genes and the differential gene expression values between RNA edited and non-edited samples.  5) 'Differential gene expression between RNA A-to-I edited versus non-edited samples' category This category provides the differential gene expressions between RNA edited and non-edited samples.  6) 'Protein coding region RNA A-to-I editings' category This category provides the editing positioning information across the main protein domains with lollipop plots.  7) 'The effects of the RNA editing to the miRNA binding sites' category This category provides the potential effects of RNA editing relating to microRNA specificity.  8) 'The effects of the RNA editing to the stability of the RNA structures' category This category provides the potential effects of RNA editing to the RNA secondary structures.  9) 'Relation with ADAR' category This category provides the correlation between ADAR gene expression and RNA editing frequency.  10) 'Relation with Cancer stages and survival state' category This category provides the correlation between survival stage and RNA editing frequency.  11) 'Related drugs and diseases with this gene' category This table provides the DrugBank information of approved drugs related with RNA edited gene. Next table provides disease information related to the RNA edited gene.   3. Download data and contact us Please go to download page and contact page. |
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