Survival analysis tools in genomics research

Human Genomics

Volumn 8, Issue 1, 2014, Pages

  Chen, Xintong ^a   Sun, Xiaochen ^a   Hoshida, Yujin ^a  

^a Division of Liver Diseases   (United States)

Author keywords

Genomic database; Software; Survival analysis; Web application

Indexed keywords

GENOMICS; PROTEIN FINGERPRINTING; REVIEW; SOFTWARE; SURVIVAL ANALYSIS; COMPUTER PROGRAM; FACTUAL DATABASE; GENE EXPRESSION PROFILING; GENETIC ASSOCIATION; GENETIC DATABASE; GENETIC MARKER; GENETICS; HUMAN; MEDICAL RESEARCH; NEOPLASM; PATHOLOGY; PROCEDURES; SURVIVAL;

GENETIC MARKER;

BIOMEDICAL RESEARCH; DATABASES, FACTUAL; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENETIC ASSOCIATION STUDIES; GENETIC MARKERS; GENOMICS; HUMANS; NEOPLASMS; SOFTWARE; SURVIVAL ANALYSIS;

EID: 84964696665     PISSN: 14739542     EISSN: 14797364     Source Type: Journal    
DOI: 10.1186/s40246-014-0021-z     Document Type: Review

References (49)

1. van't Veer LJ, Bernards R: Enabling personalized cancer medicine through analysis of gene-expression patterns. Nature 2008, 452(7187):564-570.
2. Farcomeni A: A review of modern multiple hypothesis testing, with particular attention to the false discovery proportion. Stat Methods Med Res 2008, 17(4):347-388.
3. Tusher VG, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 2001, 98(9):5116-5121.
4. Bair E, Tibshirani R: Semi-supervised methods to predict patient survival from gene expression data. PLoS Biol 2004, 2(4):E108.
5. Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP: GenePattern 2.0. Nat Genet 2006, 38(5):500-501.
6. Hoshida Y, Villanueva A, Kobayashi M, Peix J, Chiang DY, Camargo A, Gupta S, Moore J, Wrobel MJ, Lerner J, Reich M, Chan JA, Glickman JN, Ikeda K, Hashimoto M, Watanabe G, Daidone MG, Roayaie S, Schwartz M, Thung S, Salvesen HB, Gabriel S, Mazzaferro V, Bruix J, Friedman SL, Kumada H, Llovet JM, Golub TR: Gene expression in fixed tissues and outcome in hepatocellular carcinoma. N Engl J Med 2008, 359(19):1995-2004.
7. Li H, Gui J: Partial Cox regression analysis for high-dimensional microarray gene expression data. Bioinformatics 2004, 20(Suppl 1):i208-i215.
8. Zhang W, Ota T, Shridhar V, Chien J, Wu B, Kuang R: Network-based survival analysis reveals subnetwork signatures for predicting outcomes of ovarian cancer treatment. PLoS Comput Biol 2013, 9(3):e1002975.
9. Bioconductor-open source software for bioinformatics. In [http://www.bioconductor.org/]
10. Schroder MS, Culhane AC, Quackenbush J, Haibe-Kains B: survcomp: An R/Bioconductor package for performance assessment and comparison of survival models. Bioinformatics 2011, 27(22):3206-3208.
11. Significance Analysis of Microarrays-supervised learning software for genomic expression data mining. In [http://statweb.stanford.edu/~tibs/SAM/]
12. GenePattern-A powerful genomic analysis platform. In [http://www. broadinstitute.org/cancer/software/genepattern/]
13. GParc-GenePattern module repository. In [http://gparc.org/]
14. Net-Cox-network-based survival analysis reveals subnetwork signatures for predicting outcomes of ovarian cancer treatment. In [http://compbio. cs.umn.edu/Net-Cox/]
15. survcomp-performance assessment and comparison for survival analysis. In [http://www.bioconductor.org/packages/release/bioc/html/survcomp.html]
16. Gene Expression Omnibus-A public functional genomics data repository. In [http://www.ncbi.nlm.nih.gov/geo/].
17. ArrayExpress-A database of functional genomics experiments. In [http://www.ebi.ac.uk/arrayexpress/]
18. The Cancer Genome Atlas (TCGA) Data Portal; [https://tcga-data.nci.nih.gov/tcga/]
19. Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Varambally R, Yu J, Briggs BB, Barrette TR, Anstet MJ, Kincead-Beal C, Kulkarni P, Varambally S, Ghosh D, Chinnaiyan AM: Oncomine 3.0: genes, pathways, and networks in a collection of 18, 000 cancer gene expression profiles. Neoplasia 2007, 9(2):166-180.
20. Cancer Cell Line Encyclopedia (CCLE); [http://www.broadinstitute.org/ccle/home]
21. Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, Sun Y, Jacobsen A, Sinha R, Larsson E, Cerami E, Sander C, Schultz N: Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal 2013, 6(269):l1.
22. Gyorffy B, Lanczky A, Szallasi Z: Implementing an online tool for genomewide validation of survival-Associated biomarkers in ovarian-cancer using microarray data from 1287 patients. Endocr Relat Cancer 2012, 19(2):197-208.
23. Mizuno H, Kitada K, Nakai K, Sarai A: PrognoScan: A new database for meta-Analysis of the prognostic value of genes. BMC Med Genomics 2009, 2:18.
24. Ringner M, Fredlund E, Hakkinen J, Borg A, Staaf J: GOBO: gene expressionbased outcome for breast cancer online. PLoS One 2011, 6(3):e17911.
25. Gyorffy B, Benke Z, Lanczky A, Balazs B, Szallasi Z, Timar J, Schafer R: RecurrenceOnline: An online analysis tool to determine breast cancer recurrence and hormone receptor status using microarray data. Breast Cancer Res Treat 2012, 132(3):1025-1034.
26. Goswami CP, Nakshatri H: PROGgene: gene expression based survival analysis web application for multiple cancers. J Clin Bioinformatics 2013, 3(1):22.
27. Jezequel P, Campone M, Gouraud W, Guerin-Charbonnel C, Leux C, Ricolleau G, Campion L: bc-GenExMiner: An easy-To-use online platform for gene prognostic analyses in breast cancer. Breast Cancer Res Treat 2012, 131(3):765-775.
28. Elfilali A, Lair S, Verbeke C, La Rosa P, Radvanyi F, Barillot E: ITTACA: A new database for integrated tumor transcriptome array and clinical data analysis. Nucleic Acids Res 2006, 34(Database issue):D613-D616.
29. Aguirre-Gamboa R, Gomez-Rueda H, Martinez-Ledesma E, Martinez-Torteya A, Chacolla-Huaringa R, Rodriguez-Barrientos A, Tamez-Pena JG, Trevino V: SurvExpress: An online biomarker validation tool and database for cancer gene expression data using survival analysis. PLoS One 2013, 8(9):e74250.
30. Madhavan S, Gusev Y, Harris M, Tanenbaum DM, Gauba R, Bhuvaneshwar K, Shinohara A, Rosso K, Carabet LA, Song L, Riggins RB, Dakshanamurthy S, Wang Y, Byers SW, Clarke R, Weiner LM: G-DOC: A systems medicine platform for personalized oncology. Neoplasia 2011, 13(9):771-783.
31. Bilal E, Dutkowski J, Guinney J, Jang IS, Logsdon BA, Pandey G, Sauerwine BA, Shimoni Y, Moen Vollan HK, Mecham BH, Rueda OM, Tost J, Curtis C, Alvarez MJ, Kristensen VN, Aparicio S, Borresen-Dale AL, Caldas C, Califano A, Friend SH, Ideker T, Schadt EE, Stolovitzky GA, Margolin AA: Improving breast cancer survival analysis through competition-based multidimensional modeling. PLoS Comput Biol 2013, 9(5):e1003047.
32. Oncomine; [https://www.oncomine.org/resource/login.html]
33. cBioPortal for Cancer Genomics; [http://www.cbioportal.org/public-portal/]
34. Kaplan-Meier Plotter-cancer survival analysis. In [http://kmplot.com/analysis/]
35. PrognoScan-A new database for meta-Analysis of the prognostic value of genes. In [http://www.abren.net/PrognoScan/]
36. GOBO-Gene Expression-Based Outcome for Breast Cancer Online; [http://co.bmc.lu.se/gobo/]
37. Recurrence Online-Transcriptome based breast cancer diagnostics. In [http://www.recurrenceonline.com/]
38. PROGgene-Pan Cancer Prognostics Database; [http://watson.compbio.iupui. edu/chirayu/proggene/database/?url=proggene]
39. bc-GenExMiner-platform for gene prognostic analyses in breast cancer. In [http://bcgenex.centregauducheau.fr/BC-GEM/GEM-Accueil.php?js=1]
40. ITTACA-Integrated Tumor Transcriptome Array and Clinical Data Analysis; [http://bioinfo-out.curie.fr/ittaca/]
41. SurvExpress-biomarker validation for cancer gene expression. In [http://bioinformatica.mty.itesm.mx:8080/Biomatec/SurvivaX.jsp]
42. G-DOC Plus-Georgetown Database of Cancer Plus other diseases; [https://gdoc.georgetown.edu/gdoc/]
43. Hoshida Y, Moeini A, Alsinet C, Kojima K, Villanueva A: Gene signatures in the management of hepatocellular carcinoma. Semin Oncol 2012, 39:473-485.
44. McShane LM, Altman DG, Sauerbrei W, Taube SE, Gion M, Clark GM: Reporting recommendations for tumor marker prognostic studies (REMARK). J Natl Cancer Inst 2005, 97(16):1180-1184.
45. Vandenbroucke JP, von Elm E, Altman DG, Gotzsche PC, Mulrow CD, Pocock SJ, Poole C, Schlesselman JJ, Egger M, Initiative S: Strengthening the Reporting of Observational Studies in Epidemiology (STROBE): explanation and elaboration. PLoS Med 2007, 4(10):e297.
46. Bossuyt PM, Reitsma JB, Bruns DE, Gatsonis CA, Glasziou PP, Irwig LM, Moher D, Rennie D, de Vet HC, Lijmer JG, Standards for Reporting of Diagnostic Accuracy: The STARD statement for reporting studies of diagnostic accuracy: explanation and elaboration. Ann Intern Med 2003, 138(1):W1-W12.
47. Simon RM, Paik S, Hayes DF: Use of archived specimens in evaluation of prognostic and predictive biomarkers. J Natl Cancer Inst 2009, 101(21):1446-1452.
48. Koscielny S: Why most gene expression signatures of tumors have not been useful in the clinic. Sci Transl Med 2010, 2(14):14ps12.
49. Geiss GK, Bumgarner RE, Birditt B, Dahl T, Dowidar N, Dunaway DL, Fell HP, Ferree S, George RD, Grogan T, James JJ, Maysuria M, Mitton JD, Oliveri P, Osborn JL, Peng T, Ratcliffe AL, Webster PJ, Davidson EH, Hood L, Dimitrov K: Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol 2008, 26(3):317-325.