PMID- 26589293
OWN - NLM
STAT- MEDLINE
DCOM- 20161005
LR  - 20181113
IS  - 1756-994X (Electronic)
IS  - 1756-994X (Linking)
VI  - 7
DP  - 2015 Nov 20
TI  - TCLP: an online cancer cell line catalogue integrating HLA type, predicted 
      neo-epitopes, virus and gene expression.
PG  - 118
LID - 10.1186/s13073-015-0240-5 [doi]
LID - 118
AB  - Human cancer cell lines are an important resource for research and drug 
      development. However, the available annotations of cell lines are sparse, 
      incomplete, and distributed in multiple repositories. Re-analyzing publicly 
      available raw RNA-Seq data, we determined the human leukocyte antigen (HLA) type 
      and abundance, identified expressed viruses and calculated gene expression of 
      1,082 cancer cell lines. Using the determined HLA types, public databases of cell 
      line mutations, and existing HLA binding prediction algorithms, we predicted 
      antigenic mutations in each cell line. We integrated the results into a 
      comprehensive knowledgebase. Using the Django web framework, we provide an 
      interactive user interface with advanced search capabilities to find and explore 
      cell lines and an application programming interface to extract cell line 
      information. The portal is available at http://celllines.tron-mainz.de.
FAU - Scholtalbers, Jelle
AU  - Scholtalbers J
AD  - TRON - Translational Oncology at the University Medical Center of Johannes 
      Gutenberg University, Freiligrathstrasse 12, 55131, Mainz, Germany.
AD  - Present address: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, 
      Heidelberg, Germany.
FAU - Boegel, Sebastian
AU  - Boegel S
AD  - TRON - Translational Oncology at the University Medical Center of Johannes 
      Gutenberg University, Freiligrathstrasse 12, 55131, Mainz, Germany. 
      boegels@uni-mainz.de.
AD  - University Medical Center of the Johannes Gutenberg-University Mainz, 55131, 
      Mainz, Germany. boegels@uni-mainz.de.
FAU - Bukur, Thomas
AU  - Bukur T
AD  - TRON - Translational Oncology at the University Medical Center of Johannes 
      Gutenberg University, Freiligrathstrasse 12, 55131, Mainz, Germany.
AD  - University Medical Center of the Johannes Gutenberg-University Mainz, 55131, 
      Mainz, Germany.
FAU - Byl, Marius
AU  - Byl M
AD  - TRON - Translational Oncology at the University Medical Center of Johannes 
      Gutenberg University, Freiligrathstrasse 12, 55131, Mainz, Germany.
FAU - Goerges, Sebastian
AU  - Goerges S
AD  - TRON - Translational Oncology at the University Medical Center of Johannes 
      Gutenberg University, Freiligrathstrasse 12, 55131, Mainz, Germany.
FAU - Sorn, Patrick
AU  - Sorn P
AD  - TRON - Translational Oncology at the University Medical Center of Johannes 
      Gutenberg University, Freiligrathstrasse 12, 55131, Mainz, Germany.
FAU - Loewer, Martin
AU  - Loewer M
AD  - TRON - Translational Oncology at the University Medical Center of Johannes 
      Gutenberg University, Freiligrathstrasse 12, 55131, Mainz, Germany.
FAU - Sahin, Ugur
AU  - Sahin U
AD  - TRON - Translational Oncology at the University Medical Center of Johannes 
      Gutenberg University, Freiligrathstrasse 12, 55131, Mainz, Germany.
AD  - University Medical Center of the Johannes Gutenberg-University Mainz, 55131, 
      Mainz, Germany.
AD  - Biopharmaceutical New Technologies (BioNTech) Corporation, An der Goldgrube 12, 
      55131, Mainz, Germany.
FAU - Castle, John C
AU  - Castle JC
AD  - TRON - Translational Oncology at the University Medical Center of Johannes 
      Gutenberg University, Freiligrathstrasse 12, 55131, Mainz, Germany.
AD  - Present address: Agenus and 4-Antibody AG, Hochbergerstrasse 60C, CH-4057, Basel, 
      Switzerland.
LA  - eng
PT  - Journal Article
DEP - 20151120
PL  - England
TA  - Genome Med
JT  - Genome medicine
JID - 101475844
RN  - 0 (Epitopes)
RN  - 0 (HLA Antigens)
SB  - IM
MH  - Algorithms
MH  - *Cell Line, Tumor
MH  - Computational Biology/methods
MH  - *Databases, Genetic
MH  - Databases, Nucleic Acid
MH  - Epitopes/genetics/immunology
MH  - Gene Expression
MH  - HCT116 Cells
MH  - HLA Antigens/*genetics/*immunology
MH  - Humans
MH  - Information Systems
MH  - Internet
MH  - Mutation
MH  - Neoplasms/*genetics/*immunology/pathology/virology
MH  - *Online Systems
MH  - User-Computer Interface
PMC - PMC4653878
EDAT- 2015/11/22 06:00
MHDA- 2016/10/07 06:00
PMCR- 2015/11/20
CRDT- 2015/11/22 06:00
PHST- 2015/07/31 00:00 [received]
PHST- 2015/11/09 00:00 [accepted]
PHST- 2015/11/22 06:00 [entrez]
PHST- 2015/11/22 06:00 [pubmed]
PHST- 2016/10/07 06:00 [medline]
PHST- 2015/11/20 00:00 [pmc-release]
AID - 10.1186/s13073-015-0240-5 [pii]
AID - 240 [pii]
AID - 10.1186/s13073-015-0240-5 [doi]
PST - epublish
SO  - Genome Med. 2015 Nov 20;7:118. doi: 10.1186/s13073-015-0240-5.