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Table 1 Potential biologically relevant queries enabled by GFML

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