Survival analysis tools in genomics research

被引：8

作者：

Chen, Xintong ^{[1
]}

Sun, Xiaochen ^{[1
]}

Hoshida, Yujin ^{[1
]}

机构：

[1] Icahn Sch Med Mt Sinai, Dept Med, Div Liver Dis, Liver Canc Program,Tisch Canc Inst, New York, NY 10029 USA

来源：

HUMAN GENOMICS | 2014年 / 8卷

关键词：

Survival analysis; Software; Web application; Genomic database; GENE-EXPRESSION; DATABASE;

D O I：

10.1186/s40246-014-0021-z

中图分类号：

Q3 [遗传学];

学科分类号：

071007 [遗传学];

摘要：

There is an increasing demand to determine the clinical implication of experimental findings in molecular biomedical research. Survival (or failure time) analysis methodologies have been adapted to the analysis of genomics data to link molecular information with clinical outcomes of interest. Genome-wide molecular profiles have served as sources for discovery of predictive/prognostic biomarkers as well as therapeutic targets in the past decade. In this review, we overview currently available software, web applications, and databases specifically developed for survival analysis in genomics research and discuss issues in assessing clinical utility of molecular features derived from genomic profiling.

引用

页数：5

共 28 条

[1]

SurvExpress: An Online Biomarker Validation Tool and Database for Cancer Gene Expression Data Using Survival Analysis [J].

Aguirre-Gamboa, Raul ;

Gomez-Rueda, Hugo ;

Martinez-Ledesma, Emmanuel ;

Martinez-Torteya, Antonio ;

Chacolla-Huaringa, Rafael ;

Rodriguez-Barrientos, Alberto ;

Tamez-Pena, Jose G. ;

Trevino, Victor .

PLOS ONE, 2013, 8 (09)

[2]

Semi-supervised methods to predict patient survival from gene expression data [J].

Bair, E ;

Tibshirani, R .

PLOS BIOLOGY, 2004, 2 (04) :511-522

[3]

Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling [J].

Bilal, Erhan ;

Dutkowski, Janusz ;

Guinney, Justin ;

Jang, In Sock ;

Logsdon, Benjamin A. ;

Pandey, Gaurav ;

Sauerwine, Benjamin A. ;

Shimoni, Yishai ;

Vollan, Hans Kristian Moen ;

Mecham, Brigham H. ;

Rueda, Oscar M. ;

Tost, Jorg ;

Curtis, Christina ;

Alvarez, Mariano J. ;

Kristensen, Vessela N. ;

Aparicio, Samuel ;

Borresen-Dale, Anne-Lise ;

Caldas, Carlos ;

Califano, Andrea ;

Friend, Stephen H. ;

Ideker, Trey ;

Schadt, Eric E. ;

Stolovitzky, Gustavo A. ;

Margolin, Adam A. .

PLOS COMPUTATIONAL BIOLOGY, 2013, 9 (05)

[4]

Towards complete and accurate reporting of studies of diagnostic accuracy: The STARD initiative [J].

Bossuyt, PM ;

Reitsma, JB ;

Bruns, DE ;

Gatsonis, CA ;

Glasziou, PP ;

Irwig, LM ;

Lijmer, JG ;

Moher, D ;

Rennie, D ;

de Vet, HCW .

ANNALS OF INTERNAL MEDICINE, 2003, 138 (01) :40-44

[5]

ITTACA: a new database for integrated tumor transcriptome array and clinical data analysis [J].

Elfilali, Adil ;

Lair, Severine ;

Verbeke, Catia ;

La Rosa, Philippe ;

Radvanyi, Francois ;

Barillot, Emmanuel .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D613-D616

[6]

A review of modern multiple hypothesis testing, with particular attention to the false discovery proportion [J].

Farcomeni, Alessio .

STATISTICAL METHODS IN MEDICAL RESEARCH, 2008, 17 (04) :347-388

[7]

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

[8]

Direct multiplexed measurement of gene expression with color-coded probe pairs [J].

Geiss, Gary K. ;

Bumgarner, Roger E. ;

Birditt, Brian ;

Dahl, Timothy ;

Dowidar, Naeem ;

Dunaway, Dwayne L. ;

Fell, H. Perry ;

Ferree, Sean ;

George, Renee D. ;

Grogan, Tammy ;

James, Jeffrey J. ;

Maysuria, Malini ;

Mitton, Jeffrey D. ;

Oliveri, Paola ;

Osborn, Jennifer L. ;

Peng, Tao ;

Ratcliffe, Amber L. ;

Webster, Philippa J. ;

Davidson, Eric H. ;

Hood, Leroy .

NATURE BIOTECHNOLOGY, 2008, 26 (03) :317-325

[9]

Goswami Chirayu Pankaj, 2013, J Clin Bioinforma, V3, P22, DOI 10.1186/2043-9113-3-22

[10]

Implementing an online tool for genome-wide validation of survival-associated biomarkers in ovarian-cancer using microarray data from 1287 patients [J].

Gyoerffy, Balazs ;

Lanczky, Andras ;

Szallasi, Zoltan .

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