Oncofuse statistics

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Number of citations per year for the bioinformatics software tool Oncofuse
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Protocols

Oncofuse specifications

Information


Unique identifier OMICS_01406
Name Oncofuse
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A list of genomic positions of breakpoints in a pair of fusion partner genes.
Input format TSV
Output format TSV
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 1.1.1
Stability Stable
Requirements
JRE
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Francisco J. Novo

Information


Unique identifier OMICS_01406
Name Oncofuse
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Francisco J. Novo

Publications for Oncofuse

Oncofuse citations

 (8)
library_books

Actionable perturbations of damage responses by TCL1/ATM and epigenetic lesions form the basis of T PLL

2018
Nat Commun
PMCID: 5814445
PMID: 29449575
DOI: 10.1038/s41467-017-02688-6

[…] yzed using Tophat-Fusion and the associated downstream filtering pipeline (Tophat-Fusion Post). Alternatively with less stringent quality filters, but with calculation of oncogenic potential, we used oncofuse with two complementary filters: passenger probability <0.001, driver probability >0.999 and minimum support reads >10, as well as passenger probability <0.01, driver probability >0.99, and mi […]

library_books

Recurrent hyperactive ESR1 fusion proteins in endocrine therapy resistant breast cancer

2018
Ann Oncol
PMCID: 5913625
PMID: 29360925
DOI: 10.1093/annonc/mdy025

[…] lapping with both ends of the translocation only in LnM (Figure A inset), a characteristic often seen around REs [, ]. The fusion transcript is in-frame and joins ESR1 exons 1–6 with DAB2 exons 3–15. OncoFuse is a naive bayesian classifier built to predict the oncogenic potential of fusion genes [] and this showed the ESR1–DAB2 fusion to have a score of 0.99 (P < 0.0001). Notably, the location of […]

library_books

Genomic and transcriptomic heterogeneity in metaplastic carcinomas of the breast

2017
PMCID: 5711926
PMID: 29214215
DOI: 10.1038/s41523-017-0048-0

[…] scribed. deFuse and ChimeraScan were used to identify mate-pairs supporting novel chimeric transcripts as previously described (). Candidates that resulted in open reading frames were annotated using OncoFuse. Nominated in-frame fusion gene candidates, candidates identified by both deFuse and ChimeraScan, as well as those with known associated functions, and those that harbored intact functional d […]

call_split

Stapled peptide inhibitors of RAB25 target context specific phenotypes in cancer

2017
Nat Commun
PMCID: 5610242
PMID: 28939823
DOI: 10.1038/s41467-017-00888-8
call_split See protocol

[…] on counts of genes and exons, and Cufflinks was used to estimate gene expression (FPKM). Genetic variants were called using GATK unified genotyper. Fusions were detected using STAR and filtered using Oncofuse. Quality of raw and aligned reads was assessed using FastQC and Qualimap.FPKM values of six technical samples (pcDNA3-HEY + DMSO, RAB25-HEY + DMSO, RAB25-HEY + RFP14, each from individual bio […]

call_split

IL2RG, identified as overexpressed by RNA seq profiling of pancreatic intraepithelial neoplasia, mediates pancreatic cancer growth

2017
Oncotarget
PMCID: 5663522
PMID: 29137350
DOI: 10.18632/oncotarget.19848
call_split See protocol

[…] ophat-fusion ( http://ccb.jhu.edu/software/tophat/fusion_index.shtml). The fusion minimum distance was set to 100000000 and anchor length to 13. Tophat-fusion-post results were further filtered using Oncofuse (www.unav.es/genetica/oncofuse.html). Fusion events were filtered out if a fusion event was reported in a normal pancreatic duct sample, if the fusion event included a gene and partnered pseu […]

library_books

TumorNext: A comprehensive tumor profiling assay that incorporates high resolution copy number analysis and germline status to improve testing accuracy

2016
Oncotarget
PMCID: 5356550
PMID: 27626691
DOI: 10.18632/oncotarget.11910

[…] 100×, ≥ 200×, ≥ 500×, and ≥ 1000×.Annotation of variants was performed using custom scripts based on recommendations from the Human Genome Variation Society (HGVS). Gene fusions were annotated using Oncofuse v1.0.7 (ref: doi: 10.1093/bioinformatics/btt445) to report only gene fusions where one of the two fusion partners is in our target genes.The TumorNext pipeline was designed to achieve maximum […]


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Oncofuse institution(s)
LABS, Persistent Systems, Pingala-Aryabhata, Pune, India; University of Michigan, Ann Arbor, MI , USA

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