GENT2: an updated gene expression database for normal and tumor tissues

被引：325

作者：

Park, Seung-Jin ^{[1
,2
]}

Yoon, Byoung-Ha ^{[1
,2
]}

Kim, Seon-Kyu ^{[3
]}

Kim, Seon-Young ^{[1
,2
]}

机构：

[1] KRIBB, Genome Editing Res Ctr, Daejeon 34141, South Korea

[2] UST, Dept Biosci, Daejeon 34113, South Korea

[3] KRIBB, Personalized Genom Med Res Ctr, Daejeon 34141, South Korea

来源：

BMC MEDICAL GENOMICS | 2019年 / 12卷 / Suppl 5期

基金：

新加坡国家研究基金会;

关键词：

Tissue and cell line wide gene expression profiling; Cancer subtype profiling; Survival analysis; Meta-survival analysis; Large scale microarray web-database; CANCER;

D O I：

10.1186/s12920-019-0514-7

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

BackgroundGene Expression database of Normal and Tumor tissues 2 (GENT2) is an updated version of GENT, which has provided a user-friendly search platform for gene expression patterns across different normal and tumor tissues compiled from public gene expression data sets.ResultsWe refactored GENT2 with recent technologies such as Apache Lucene indexing for fast search and Google Web Toolkit (GWT) framework for a user-friendly web interface. Now, GENT2 contains more than 68,000 samples and has several new useful functions. First, GENT2 now provides gene expression across 72 different tissues compared to 57 in GENT. Second, with increasing importance of tumor subtypes, GENT2 provides an option to study the differential expression and its prognostic significance based on tumor subtypes. Third, whenever available, GENT2 provides prognostic information of a gene of interest. Fourth, GENT2 provides a meta-analysis of survival information to provide users more reliable prognostic value of a gene of interest.ConclusionsIn conclusion, with these significant improvements, GENT2 will continue to be a useful tool to a wide range of researchers. GENT2 is freely available at http://gent2.appex.kr.

引用

页数：8

共 20 条

[1] HER2 and EGFR Overexpression Support Metastatic Progression of Prostate Cancer to Bone [J].

Day, Kathleen C. ;

Hiles, Guadalupe Lorenzatti ;

Kozminsky, Molly ;

Dawsey, Scott J. ;

Paul, Alyssa ;

Broses, Luke J. ;

Shah, Rajal ;

Kunja, Lakshmi P. ;

Hall, Christopher ;

Palanisamy, Nallasivam ;

Daignault-Newton, Stephanie ;

El-Sawy, Layla ;

Wilson, Steven James ;

Chou, Andrew ;

Ignatoski, Kathleen Woods ;

Keller, Evan ;

Thomas, Dafydd ;

Nagrath, Sunitha ;

Morgan, Todd ;

Day, Mark L. .

CANCER RESEARCH, 2017, 77 (01) :74-85

[2] Multifactorial Approach to Predicting Resistance to Anthracyclines [J].

Desmedt, Christine ;

Di Leo, Angelo ;

de Azambuja, Evandro ;

Larsimont, Denis ;

Haibe-Kains, Benjamin ;

Selleslags, Jean ;

Delaloge, Suzette ;

Duhem, Caroline ;

Kains, Jean-Pierre ;

Carly, Birgit ;

Maerevoet, Marie ;

Vindevoghel, Anita ;

Rouas, Ghislane ;

Lallemand, Francoise ;

Durbecq, Virginie ;

Cardoso, Fatima ;

Salgado, Roberto ;

Rovere, Rodrigo ;

Bontempi, Gianluca ;

Michiels, Stefan ;

Buyse, Marc ;

Nogaret, Jean-Marie ;

Qi, Yuan ;

Symmans, Fraser ;

Pusztai, Lajos ;

D'Hondt, Veronique ;

Piccart-Gebhart, Martine ;

Sotiriou, Christos .

JOURNAL OF CLINICAL ONCOLOGY, 2011, 29 (12) :1578-1586

[3] BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery [J].

Dingerdissen, Hayley M. ;

Torcivia-Rodriguez, John ;

Hu, Yu ;

Chang, Ting-Chia ;

Mazumder, Raja ;

Kahsay, Robel .

NUCLEIC ACIDS RESEARCH, 2018, 46 (D1) :D1128-D1136

[4] Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal [J].

Gao, Jianjiong ;

Aksoy, Buelent Arman ;

Dogrusoz, Ugur ;

Dresdner, Gideon ;

Gross, Benjamin ;

Sumer, S. Onur ;

Sun, Yichao ;

Jacobsen, Anders ;

Sinha, Rileen ;

Larsson, Erik ;

Cerami, Ethan ;

Sander, Chris ;

Schultz, Nikolaus .

SCIENCE SIGNALING, 2013, 6 (269) :pl1

[5] affy -: analysis of Affymetrix GeneChip data at the probe level [J].

Gautier, L ;

Cope, L ;

Bolstad, BM ;

Irizarry, RA .

BIOINFORMATICS, 2004, 20 (03) :307-315

[6] Comprehensive molecular portraits of human breast tumours [J].

Koboldt, Daniel C. ;

Fulton, Robert S. ;

McLellan, Michael D. ;

Schmidt, Heather ;

Kalicki-Veizer, Joelle ;

McMichael, Joshua F. ;

Fulton, Lucinda L. ;

Dooling, David J. ;

Ding, Li ;

Mardis, Elaine R. ;

Wilson, Richard K. ;

Ally, Adrian ;

Balasundaram, Miruna ;

Butterfield, Yaron S. N. ;

Carlsen, Rebecca ;

Carter, Candace ;

Chu, Andy ;

Chuah, Eric ;

Chun, Hye-Jung E. ;

Coope, Robin J. N. ;

Dhalla, Noreen ;

Guin, Ranabir ;

Hirst, Carrie ;

Hirst, Martin ;

Holt, Robert A. ;

Lee, Darlene ;

Li, Haiyan I. ;

Mayo, Michael ;

Moore, Richard A. ;

Mungall, Andrew J. ;

Pleasance, Erin ;

Robertson, A. Gordon ;

Schein, Jacqueline E. ;

Shafiei, Arash ;

Sipahimalani, Payal ;

Slobodan, Jared R. ;

Stoll, Dominik ;

Tam, Angela ;

Thiessen, Nina ;

Varhol, Richard J. ;

Wye, Natasja ;

Zeng, Thomas ;

Zhao, Yongjun ;

Birol, Inanc ;

Jones, Steven J. M. ;

Marra, Marco A. ;

Cherniack, Andrew D. ;

Saksena, Gordon ;

Onofrio, Robert C. ;

Pho, Nam H. .

NATURE, 2012, 490 (7418) :61-70

[7] CellLineNavigator: a workbench for cancer cell line analysis [J].

Krupp, Markus ;

Itzel, Timo ;

Maass, Thorsten ;

Hildebrandt, Andreas ;

Galle, Peter R. ;

Teufel, Andreas .

NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D942-D948

[8] RNA-Seq Atlas-a reference database for gene expression profiling in normal tissue by next-generation sequencing [J].

Krupp, Markus ;

Marquardt, Jens U. ;

Sahin, Ugur ;

Galle, Peter R. ;

Castle, John ;

Teufel, Andreas .

BIOINFORMATICS, 2012, 28 (08) :1184-1185

[9] Oncopression: gene expression compendium for cancer with matched normal tissues [J].

Lee, Jungsul ;

Choi, Chulhee .

BIOINFORMATICS, 2017, 33 (13) :2068-2070

[10] Transcriptomic analysis of mitochondrial TFAM depletion changing cell morphology and proliferation [J].

Lee, Woo Rin ;

Na, Heeju ;

Lee, Seon Woo ;

Lim, Won-Jun ;

Kim, Namshin ;

Lee, J. Eugene ;

Kang, Changwon .

SCIENTIFIC REPORTS, 2017, 7

← 1 2 →