FPIA: A database for gene fusion profiling and interactive analyses

Abstract

As one of the hallmarks of cancer, gene fusions play an important role in tumorigenesis, and have been established as biomarkers and therapeutic targets. Although recent years have witnessed the development of gene fusion databases, a tool with interactive analytic functions remains lacking. Here, we introduce fusion profiling interactive analysis (FPIA), a web server to perform interactive and customizable analysis on fusion genes. With this platform, researchers can easily explore fusion‐associated biological and molecular differences including gene expression, tumor purity and ploidy, mutation, copy number variations, protein expression, immune cell infiltration, stemness, telomere length, microsatellite instability, survival and novel peptides based on 33 cancer types from The Cancer Genome Atlas (TCGA) data. Currently, it contains 31 633 fusion events from 6910 patients. FPIA complements the existing gene fusion annotation databases with its multiomics analytic capacity, integrated analysis features, customized analysis selection and user‐friendly design. The comprehensive data analyses by FPIA will greatly facilitate data mining, hypothesis generation and therapeutic target discovery. FPIA is available at http://bioinfo-sysu.com/fpia.

REIA: A database for cancer A-to-I RNA editing with interactive analysis

“…(2) In terms of analysis, REIA is advantageous to many prior works not only because it is interactive but also because it is multi-functional. On one hand, similar to our previous work, a key enabler for the interactive analysis is the model-view-controller (MVC) framework 22 . Unlike prior databases that were mostly using bootstrap 14 , 23 , REIA here applies MVC to handle user interface, business logic, and data management in a divide-and-conquer fashion, which makes the interaction and maintenance much easier.…”

Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes

“…For some groups of variants, especially fusion proteins, HGVS guidelines are lacking. Reactome’s fusion protein nomenclature system can improve standardization of fusion protein annotations by HGVS and emerging fusion protein databases FusionGDB [75], CIViC [76], and FPIA [77].…”

Whole exome sequencing of well-differentiated liposarcoma and dedifferentiated liposarcoma in older woman: a case report

“…Furthermore, the association between gene expression and survival was analyzed using Cox’s analysis with the “survival” packages. In addition, fusion gene events were identified based on multiple online fusion gene databases (FPIA ( 27 ), ChimerDB 4.0 ( 28 ), and TCGA Fusion Gene Database ( 29 )), and further prognostic analysis was performed with the KM method.…”