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Data released on May 15, 2018

Supporting data for "Massive NGS Data Analysis Reveals Hundreds Of Potential Novel Gene Fusions in Human Cell Lines"

Gioiosa, S; Bolis, M; Flati, T; Massini, A; Garattini, E; Chillemi, G; Fratelli, M; Castrignanò, T (2018): Supporting data for "Massive NGS Data Analysis Reveals Hundreds Of Potential Novel Gene Fusions in Human Cell Lines" GigaScience Database. RIS BibTeX Text

Gene fusions derive from chromosomal rearrangements and the resulting chimeric transcripts are often endowed with oncogenic potential. Furthermore, they serve as diagnostic tools for the clinical classification of cancer subgroups with different prognosis and, in some cases, they can provide specific drug targets. So far, many efforts have been carried out to study gene fusion events occurring in tumor samples. In recent years, the availability of a comprehensive Next Generation Sequencing dataset for all the existing human tumor cell lines has provided the opportunity to further investigate these data in order to identify novel and still uncharacterized gene fusion events. In our work, we have extensively reanalyzed 935 paired-end RNA-seq experiments downloaded from "The Cancer Cell Line Encyclopedia" repository, aiming at addressing novel putative cell-line specific gene fusion events in human malignancies. The bioinformatics analysis has been performed by the execution of four different gene fusion detection algorithms. The results have been further prioritized by running a bayesian classifier which makes an in silico validation. The collection of fusion events supported by all of the predictive softwares results in a robust set of ~1,700 in-silico predicted novel candidates suitable for downstream analyses. Given the huge amount of data and information produced, computational results have been systematized in a database named LiGeA. The database can be browsed through a dynamical and interactive web portal, further integrated with validated data from other well known repositories. Taking advantage of the intuitive query forms, the users can easily access, navigate, filter and select the putative gene fusions for further validations and studies. They can also find suitable experimental models for a given fusion of interest. We believe that the LiGeA resource can represent not only the first compendium of both known and putative novel gene fusion events in the catalog of all of the human malignant cell lines, but it can also become a handy starting point for wet-lab biologists who wish to investigate novel cancer biomarkers and specific drug targets.

Contact Submitter

Additional information:



database human gene fusions malignant cell lines ngs gene fusion detection algorithms chromosomal rearrangements bioinformatics 




  • Funding body - Fondazione Italo Monzino
  • Location - Italy
  • Award ID - 17058
  • Awardee - Maddalena Fratelli
  • Funding body - ELIXIR-IIB
  • Location - Italy
  • Award ID - 05/AR/2016-IBBE-BA
  • Comment - Efficient allocation of HPC bioinformatics resources through a federation of Galaxy webbased infrastructures (Elixir-ITA project)
  • Awardee - Tiziano Flati
  • Funding body - ELIXIR-IIB
  • Location - Italy
  • Award ID - 08/AR/2016-IBBE-BA
  • Comment - Efficient implemenation and distribution of HPC bioinformatics resources for Elixir scientific community (Elixir-ITA project)
  • Awardee - Silvia Gioiosa

Samples: Table Settings


Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
CCLE_0919606HumanhumanHomo sapiens Description:Cell line from Cervical squamous cell ...
Disease status:Cervical squamous cell carcinoma an...
Cell type:HEC108
CCLE_0929606HumanhumanHomo sapiens Description:Cell line from Esophageal carcinoma CO...
Disease status:Esophageal carcinoma
Cell type:COLO680N
CCLE_0939606HumanhumanHomo sapiens Description:Cell line from Chronic Lymphocytic Leu...
Disease status:Chronic Lymphocytic Leukemia
Cell type:KYO1
CCLE_0949606HumanhumanHomo sapiens Description:Cell line from Ovarian serous cystaden...
Disease status:Ovarian serous cystadenocarcinoma
Cell type:ES2
CCLE_0959606HumanhumanHomo sapiens Description:Cell line from Chronic Lymphocytic Leu...
Disease status:Chronic Lymphocytic Leukemia
Cell type:MONOMAC6
CCLE_0969606HumanhumanHomo sapiens Description:Cell line from Mesothelioma ACCMESO1
Disease status:Mesothelioma
Cell type:ACCMESO1
CCLE_0979606HumanhumanHomo sapiens Description:Cell line from Lung squamous cell carc...
Disease status:Lung squamous cell carcinoma
Cell type:CAL12T
CCLE_0989606HumanhumanHomo sapiens Description:Cell line from Lymphoid Neoplasm Diffu...
Disease status:Lymphoid Neoplasm Diffuse Large B-c...
Cell type:P3HR1
CCLE_0999606HumanhumanHomo sapiens Description:Cell line from Brain Lower Grade Gliom...
Disease status:Brain Lower Grade Glioma
Cell type:NB1
CCLE_1009606HumanhumanHomo sapiens Description:Cell line from Pancreatic adenocarcino...
Disease status:Pancreatic adenocarcinoma
Cell type:PATU8988S
Displaying 91-100 of 935 Sample(s).

Files: (FTP site) Table Settings


File Description
Sample ID
Data Type
File Format
Release Date
Download Link
File Attributes

File NameSample IDData TypeFile FormatSizeRelease Date 
Tabular DataTAR87.86 MB2018-04-30
GitHub archivearchive412.28 KB2018-04-30
ReadmeTEXT3.15 KB2018-04-30
Displaying 1-3 of 3 File(s).



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