Note: This repository is not frequantly updated.

Intro

AGFusion (pronounced 'A G Fusion') is an interactive web app for annotating gene fusions from the human or mouse genomes. The app is available at https://www.agfusion.app/. There is also a companion Python package.

AGFusion simply needs the reference genome, the two gene partners, and the fusion junction coordinates as input, and outputs the following:

• FASTA files of cDNA, CDS, and protein sequences.
• Visualizes the protein domain and exon architectures of the fusion transcripts.
• Saves tables listing the coordinates of protein features and exons included in the fusion.
• Optional exon structure and protein domain visualization of the wild-type version of the fusion gene partners.

Usage

AGFusion automatically predicts the functional effect of the gene fusion (e.g. in-frame, out-of-frame, etc.). Annotation is by default done only for canonical gene isoforms, but there is the option to annotate all non-canonical isoform combinations. Lastly, all gene and protein annotation is from Ensembl (up to release 95).

Input

There are two ways to provide input.

(1) Single input

The software only needs the following pieces of data per fusion:

• 5' gene partner.
• 5' gene partner junction location.
• 3' gene partner.
• 3' gene partner junction location.
• The reference genome used to call fusions (human and mouse is supported).

(2) Bulk input

Alternatively, you can provide either a generic TSV/CSV-formatted file or the output file from one of the supported fusion finding-algorithms:

• Bellerophontes
• Chimerascan
• ChimeRScope
• DeFuse
• EricScript
• FusionCatcher
• FusionInspector
• FusionMap
• JAFFA
• MapSplice
• STARFusion
• TopHatFusion

If your fusion-finding algorithm is not supported, you can either ask me to add support or just format it into a simple CSV or TSV file. Each row in the file should contain one fusion like so: gene1,gene1Junction,gene2,gene2Junction (e.g. FGFR2,1231231,DNM3,522312).

Output

Prediction

• Functional effect of the gene fusion (e.g. in-frame, out-of-frame, etc.)
• Annotates proteins with domains (e.g. PFAM database and others).

Downloadable data

• FASTA files of cDNA, CDS, and protein sequences.
• Plots of protein domain and exon architectures.
• Various tables containing many additional details about the fusion(s), including protein domain data, exon structures, etc.

Interactive figures and tables

• Table 1: All fusions.
• Table 2: Detail view.
• Protein/exon figures.
• Supports output files from fusion-finding tools.