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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. http://dx.doi.org/10.5524/100442 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:

http://hpc-bioinformatics.cineca.it/fusion/

https://github.com/tflati/fusion

Projects:


Keywords:

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

Genomic

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Funding:

  • 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

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
CCLE_0029606HumanhumanHomo sapiens Description:Cell line from Liver hepatocellular ca...
Disease status:Liver hepatocellular carcinoma
Cell type:SNU1196
...
+
CCLE_0039606HumanhumanHomo sapiens Description:Cell line from Breast invasive carcino...
Disease status:Breast invasive carcinoma
Cell type:HCC2157
...
+
CCLE_0049606HumanhumanHomo sapiens Description:Cell line from Sarcoma RH30
Disease status:Sarcoma
Cell type:RH30
...
+
CCLE_0059606HumanhumanHomo sapiens Description:Cell line from Pancreatic adenocarcino...
Disease status:Pancreatic adenocarcinoma
Cell type:PATU8988T
...
+
CCLE_0069606HumanhumanHomo sapiens Description:Cell line from Skin Cutaneous Melanoma...
Disease status:Skin Cutaneous Melanoma
Cell type:MELHO
...
+
CCLE_0079606HumanhumanHomo sapiens Description:Cell line from Ovarian serous cystaden...
Disease status:Ovarian serous cystadenocarcinoma
Cell type:OAW28
...
+
CCLE_0089606HumanhumanHomo sapiens Description:Cell line from Pancreatic adenocarcino...
Disease status:Pancreatic adenocarcinoma
Cell type:AsPC1
...
+
CCLE_0099606HumanhumanHomo sapiens Description:Cell line from Ovarian serous cystaden...
Disease status:Ovarian serous cystadenocarcinoma
Cell type:OV90
...
+
CCLE_0109606HumanhumanHomo sapiens Description:Cell line from Colon adenocarcinoma GP...
Disease status:Colon adenocarcinoma
Cell type:GP2d
...
+
CCLE_0019606HumanhumanHomo sapiens Description:Cell line from Sarcoma TE441T
Disease status:Sarcoma
Cell type:TE441T
...
+
Displaying 1-10 of 935 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
Data Type
File Format
Size
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).

History:

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