TACCO, a Database Connecting Transcriptome Alterations, Pathway Alterations and Clinical Outcomes in Cancers

Overview

Journal Sci Rep

Specialty Science

Date 2019 Mar 9

PMID 30846808

Citations 17

Authors

Po-Hao Chou

Wei-Chao Liao

Kuo-Wang Tsai

Ku-Chung Chen

Jau-Song Yu

Ting-Wen Chen

Affiliations

Soon will be listed here.

Abstract

Because of innumerable cancer sequencing projects, abundant transcriptome expression profiles together with survival data are available from the same patients. Although some expression signatures for prognosis or pathologic staging have been identified from these data, systematically discovering such kind of expression signatures remains a challenge. To address this, we developed TACCO (Transcriptome Alterations in CanCer Omnibus), a database for identifying differentially expressed genes and altered pathways in cancer. TACCO also reveals miRNA cooperative regulations and supports construction of models for prognosis. The resulting signatures have great potential for patient stratification and treatment decision-making in future clinical applications. TACCO is freely available at http://tacco.life.nctu.edu.tw/ .

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References

Osada H, Takahashi T . let-7 and miR-17-92: small-sized major players in lung cancer development. Cancer Sci. 2010; 102(1):9-17. DOI: 10.1111/j.1349-7006.2010.01707.x. View

Thompson T, Lewis J, Dejneka N, Severs W, Polavarapu R, Billingsley M . Induction of apoptosis by organotin compounds in vitro: neuronal protection with antisense oligonucleotides directed against stannin. J Pharmacol Exp Ther. 1996; 276(3):1201-16. View

Leng N, Dawson J, Thomson J, Ruotti V, Rissman A, Smits B . EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics. 2013; 29(8):1035-43. PMC: 3624807. DOI: 10.1093/bioinformatics/btt087. View

Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K . KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 2016; 45(D1):D353-D361. PMC: 5210567. DOI: 10.1093/nar/gkw1092. View

Subramanian A, Tamayo P, Mootha V, Mukherjee S, Ebert B, Gillette M . Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005; 102(43):15545-50. PMC: 1239896. DOI: 10.1073/pnas.0506580102. View

Wong N, Khwaja S, Baker C, Gay H, Thorstad W, Daly M . Prognostic microRNA signatures derived from The Cancer Genome Atlas for head and neck squamous cell carcinomas. Cancer Med. 2016; 5(7):1619-28. PMC: 4944889. DOI: 10.1002/cam4.718. View

Peter M . Targeting of mRNAs by multiple miRNAs: the next step. Oncogene. 2010; 29(15):2161-4. DOI: 10.1038/onc.2010.59. View

Jacobsen A, Silber J, Harinath G, Huse J, Schultz N, Sander C . Analysis of microRNA-target interactions across diverse cancer types. Nat Struct Mol Biol. 2013; 20(11):1325-32. PMC: 3982325. DOI: 10.1038/nsmb.2678. View

Yerukala Sathipati S, Ho S . Identifying the miRNA signature associated with survival time in patients with lung adenocarcinoma using miRNA expression profiles. Sci Rep. 2017; 7(1):7507. PMC: 5548864. DOI: 10.1038/s41598-017-07739-y. View

10.

Ternes N, Rotolo F, Michiels S . Robust estimation of the expected survival probabilities from high-dimensional Cox models with biomarker-by-treatment interactions in randomized clinical trials. BMC Med Res Methodol. 2017; 17(1):83. PMC: 5441049. DOI: 10.1186/s12874-017-0354-0. View

11.

Ahmed M, Nguyen H, Lai T, Kim D . miRCancerdb: a database for correlation analysis between microRNA and gene expression in cancer. BMC Res Notes. 2018; 11(1):103. PMC: 5822626. DOI: 10.1186/s13104-018-3160-9. View

12.

Mogilyansky E, Rigoutsos I . The miR-17/92 cluster: a comprehensive update on its genomics, genetics, functions and increasingly important and numerous roles in health and disease. Cell Death Differ. 2013; 20(12):1603-14. PMC: 3824591. DOI: 10.1038/cdd.2013.125. View

13.

Shao T, Wang G, Chen H, Xie Y, Jin X, Bai J . Survey of miRNA-miRNA cooperative regulation principles across cancer types. Brief Bioinform. 2018; 20(5):1621-1638. DOI: 10.1093/bib/bby038. View

14.

Liu F, Zhang F, Li X, Liu Q, Liu W, Song P . Prognostic role of miR-17-92 family in human cancers: evaluation of multiple prognostic outcomes. Oncotarget. 2017; 8(40):69125-69138. PMC: 5620325. DOI: 10.18632/oncotarget.19096. View

15.

Friedman J, Hastie T, Tibshirani R . Regularization Paths for Generalized Linear Models via Coordinate Descent. J Stat Softw. 2010; 33(1):1-22. PMC: 2929880. View

16.

Grossman R, Heath A, Ferretti V, Varmus H, Lowy D, Kibbe W . Toward a Shared Vision for Cancer Genomic Data. N Engl J Med. 2016; 375(12):1109-12. PMC: 6309165. DOI: 10.1056/NEJMp1607591. View

17.

Tang Z, Li C, Kang B, Gao G, Li C, Zhang Z . GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Res. 2017; 45(W1):W98-W102. PMC: 5570223. DOI: 10.1093/nar/gkx247. View

18.

Kozomara A, Griffiths-Jones S . miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2013; 42(Database issue):D68-73. PMC: 3965103. DOI: 10.1093/nar/gkt1181. View

19.

Li J, Chen Z, Tian L, Zhou C, He M, Gao Y . LncRNA profile study reveals a three-lncRNA signature associated with the survival of patients with oesophageal squamous cell carcinoma. Gut. 2014; 63(11):1700-10. PMC: 4215280. DOI: 10.1136/gutjnl-2013-305806. View

20.

Muniategui A, Pey J, Planes F, Rubio A . Joint analysis of miRNA and mRNA expression data. Brief Bioinform. 2012; 14(3):263-78. DOI: 10.1093/bib/bbs028. View