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1. Exon skipping information for TCGA and GTEx2. ORF annotation
3. Analyses of protean functional feature retention
4. sQTM analysis (Splicing Quantitative Trait Loci)
5. Understanding annotation of ExonSkipDB
Search page, example: MET
Exon skipped gene search result page
Exon skipped gene annotation result page
1) Gene summary
2) Gene structures and expression levels
3) Exon skipping events with PSIs in TCGA
4) Exon skipping events with PSIs in GTEx
5) Open reading frame (ORF) annotation in the exon skipping event
6) Exon skipping events in the canonical protein sequence
7) SNVs in the skipped exons with depth of coverage
8) Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
9) Splicing Quantitative Trait Methylation (sQTM) in the skipped exon
10) Related drugs with this gene
11) Related diseases with this gene
5. Download data and contact us
1. Exon skipping information for TCGA and GTEx
We downloaded the exon skippping event information of 8,705 patients across 33 cancer types from TCGA and of over 3,000 normal samples across 31 different tissues from GTEx(Kahles A et al. 2018). We only used the exon skipping events when they have conserved loci among the six splice sites of three exons, which involved in exon skipping such as upstream exon-skipped exon-downstream exon. Of these six sites, the four sites are the upstream exon’s donor site, skipped exons' acceptor and donor sitex, and the acceptor site of downstream exon. Based on the GENCODE v19 annotation reference genome, we have obtained 90,616 and 89,845 annotated gene structure-based exon skipping events from TCGA and GTEx, respectively.
2. ORF annotation
We examined the open reading frames of major isoforms' transcript sequences when there is the specific exon skipping event. When both of the nucleotide start and end positions of exon skipping are located inside of the coding region (CDS) and the number of transcript sequences after exclusion of the skipped exon sequence is a multiple of three, then we reported such exon skipped gene isoform as ‘in-frame’. If there are one or two nucleotide insertions, then we reported such transcript as ‘frame-shift’.
3. Protean features (domains) retention analysis
We searched the retention of 39 protein features of UniProt (6 molecule processing features, 13 region features, the 4 site features, 6 amino acid modification features, 2 natural variation features, 5 experimental info features, and 3 secondary structure features) at the canonical amino acid sequence level with skipped exon loci information. Detailed information about all of the protein features is in UniProt.
4. sQTM analysis (Splicing Quantitative Trait Loci)
The image below shows the working flow of our sQTM analysis.
5. Understanding ExonSkipDB's annotation categories
Search page, example: MET
- Input query: Official HUGO gene symbol or Entrez gene ID.
Exon skipped gene search result page
Select your gene from the gene list.
Exon skipped gene annotation result page
These are ExonSkipDB's annotation categories for your query with links to their corresponding annotation parts.
1) Gene summary category
This category shows the information of the exon skipped 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) 'Gene structures and expression levels' category
This category provides the known gene isoform models based on GENCODE basic v.19 with expression levels in pan-cancer (TCGA) and normal tissues (GTEx).
3) 'Exon skipping events with PSIs in TCGA' category
This category provides the detailed exon skipping event information including genomic location with accordant gene isoforms with four splice site matched cases (1st exon's end site, skipped exon's start and end sites, and 3rd exon's start site). Furthermore, this category shows the image of locational map of individual exon skipping events across the canonical gene isoform structure with following the averaged PSI values across in TCGA pan-cancer.
4) 'Exon skipping events with PSIs in GTEx' category
This category provides the detailed exon skipping event information including genomic location with accordant gene isoforms with four splice site matched cases (1st exon's end site, skipped exon's start and end sites, and 3rd exon's start site). Furthermore, this category shows the image of locational map of individual exon skipping events across the canonical gene isoform structure with following the averaged PSI values across in GTEx tissues.
5) 'Open reading frame (ORF) annotation in the exon skipping event' category
This category provides the annotation of the ORF of individual exon skipping events based on the major gene isoform structure.
6) 'Exon skipping events in the canonical protein sequence' category
This category provides the detailed information of the protein functional feataures based on the canonical protein sequence. It shows the unique image of presenting skipped exons in the known gene isoforms or novel isoforms through TCGA and GTEx. The gray colored background bar through this image is the region of an individual exon skipping event in the canonical protein amino acid sequences. The following table shows the genomic position, transcribed loci, and tranlated loci information of each exon skipping event. From the next table, the user can recognize which functional features were lost due to each exon skipping event. This analysis is done for the in-frame exon skipping events only.
7) 'SNVs in the skipped exons with depth of coverage' category
This category provides the information of mutations associated with exon skipping events. We checked mutations of splice site, nonsense, and frame-shift located in skipped exons. The lollipop plot shows the location on protein domains. With the detailed information of mutation, this category also shows the depth of coverage plot based on three exons, which were involved in the exon skipping event.
8) 'Splicing Quantitative Trait Loci (sQTLs) in the skipped exons' category
This category provides the information of sQTLs which are located in skipped exon regions.
9) 'Splicing Quantitative Trait Methylation (sQTM) in the skipped exon' category
This category provides the information of sQTMs. The first image shows the differential gene expressions among the cancer samples with different methylations in the first two exons from three exons involved in exon skipping events. The second image shows the pan-cancer analysis based survival plots of found sQTM events.
10) 'Related drugs with this gene category'
This table provides the DrugBank information of approved drugs related with exon skipped gene.
11) 'Related diseases with this gene' category
This table provides disease information related to the exon skipped gene.
6. Download data and contact us
Please go to download page and contact page.
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)