From: Gene Fusion Markup Language: a prototype for exchanging gene fusion data
 | Usage scenario | Example |
---|---|---|
Clinicians | Gene identifier | Lists fusion candidates that involve ERG |
Sample type | Lists prostate tissue candidates | |
Clinical significance | Lists leiomyosarcoma candidates | |
Reference | Pubmed ID/author information | |
Molecular Biologists | Protein domain | Lists fusion candidates with kinase domain |
Break in specific domain | Lists fusion that breaks or loses the SH2\SH3 domain | |
Domain with specific region | Lists fusion candidates with 3’ kinase domain | |
ORF status | Lists fusion candidates with potential ORF | |
Validation status platform | Lists fusion candidates with validation status by FISH | |
Splice pattern | Lists non-canonical splice pattern | |
Fusion product | Lists potential fusion proteins/truncated proteins | |
Fusion mechanism | Lists potential inversion | |
Splice boundary | Lists 5’ inter-genic fusion (splice boundary) | |
Bionform-aticians | Sequencing platform | Lists candidates from Illumina |
Sequence evidence | Lists candidates with sequence evidence | |
Mapping/fusion algorithm | Lists candidates detected using Bowtie + Shortfuse algorithm | |
RPKM/unique count | Lists candidates above 50 RPKM |