TANRIC: An Interactive Open Platform to Explore the Function of LncRNAs in Cancer

Overview

Journal Cancer Res

Specialty Oncology

Date 2015 Jul 26

PMID 26208906

Citations 319

Authors

Jun Li

Leng Han

Paul Roebuck

Lixia Diao

Lingxiang Liu

Yuan Yuan

John N Weinstein

Han Liang

Affiliations

Soon will be listed here.

Abstract

Long noncoding RNAs (lncRNA) have emerged as essential players in cancer biology. Using recent large-scale RNA-seq datasets, especially those from The Cancer Genome Atlas (TCGA), we have developed "The Atlas of Noncoding RNAs in Cancer" (TANRIC; http://bioinformatics.mdanderson.org/main/TANRIC:Overview), a user-friendly, open-access web resource for interactive exploration of lncRNAs in cancer. It characterizes the expression profiles of lncRNAs in large patient cohorts of 20 cancer types, including TCGA and independent datasets (>8,000 samples overall). TANRIC enables researchers to rapidly and intuitively analyze lncRNAs of interest (annotated lncRNAs or any user-defined ones) in the context of clinical and other molecular data, both within and across tumor types. Using TANRIC, we have identified a large number of lncRNAs with potential biomedical significance, many of which show strong correlations with established therapeutic targets and biomarkers across tumor types or with drug sensitivity across cell lines. TANRIC represents a valuable tool for investigating the function and clinical relevance of lncRNAs in cancer, greatly facilitating lncRNA-related biologic discoveries and clinical applications.

Citing Articles

Non-Coding RNAs in Cancer: Structure, Function, and Clinical Application.

Marton E, Varga A, Domoszlai D, Buglyo G, Balazs A, Penyige A Cancers (Basel). 2025; 17(4).

PMID: 40002172 PMC: 11853212. DOI: 10.3390/cancers17040579.

Localization is the key to action: regulatory peculiarities of lncRNAs.

Poloni J, Oliveira F, Feltes B Front Genet. 2024; 15:1478352.

PMID: 39737005 PMC: 11683014. DOI: 10.3389/fgene.2024.1478352.

Computational Prediction of Gene Regulation by lncRNAs.

Sinha T, Sadhukhan S, Panda A Methods Mol Biol. 2024; 2883:343-362.

PMID: 39702716 DOI: 10.1007/978-1-0716-4290-0_15.

Unveiling Long Non-coding RNA Networks from Single-Cell Omics Data Through Artificial Intelligence.

Cao G, Chen D Methods Mol Biol. 2024; 2883:257-279.

PMID: 39702712 DOI: 10.1007/978-1-0716-4290-0_11.

TREMSUCS-TCGA - an integrated workflow for the identification of biomarkers for treatment success.

Balogh G, Jorge N, Dupain C, Kamal M, Servant N, Le Tourneau C J Integr Bioinform. 2024; 21(4).

PMID: 39654143 PMC: 11698617. DOI: 10.1515/jib-2024-0031.

References

Rinn J, Kertesz M, Wang J, Squazzo S, Xu X, Brugmann S . Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell. 2007; 129(7):1311-23. PMC: 2084369. DOI: 10.1016/j.cell.2007.05.022. View

Mortazavi A, Williams B, McCue K, Schaeffer L, Wold B . Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008; 5(7):621-8. DOI: 10.1038/nmeth.1226. View

Dinger M, Pang K, Mercer T, Crowe M, Grimmond S, Mattick J . NRED: a database of long noncoding RNA expression. Nucleic Acids Res. 2008; 37(Database issue):D122-6. PMC: 2686506. DOI: 10.1093/nar/gkn617. View

Gupta R, Shah N, Wang K, Kim J, Horlings H, Wong D . Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature. 2010; 464(7291):1071-6. PMC: 3049919. DOI: 10.1038/nature08975. View

Wilkerson M, Hayes D . ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics. 2010; 26(12):1572-3. PMC: 2881355. DOI: 10.1093/bioinformatics/btq170. View

Yap K, Li S, Munoz-Cabello A, Raguz S, Zeng L, Mujtaba S . Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol Cell. 2010; 38(5):662-74. PMC: 2886305. DOI: 10.1016/j.molcel.2010.03.021. View

Bernard D, Prasanth K, Tripathi V, Colasse S, Nakamura T, Xuan Z . A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. EMBO J. 2010; 29(18):3082-93. PMC: 2944070. DOI: 10.1038/emboj.2010.199. View

Tripathi V, Ellis J, Shen Z, Song D, Pan Q, Watt A . The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell. 2010; 39(6):925-38. PMC: 4158944. DOI: 10.1016/j.molcel.2010.08.011. View

Wapinski O, Chang H . Long noncoding RNAs and human disease. Trends Cell Biol. 2011; 21(6):354-61. DOI: 10.1016/j.tcb.2011.04.001. View

10.

Wang D, Garcia-Bassets I, Benner C, Li W, Su X, Zhou Y . Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature. 2011; 474(7351):390-4. PMC: 3117022. DOI: 10.1038/nature10006. View

11.

Prensner J, Iyer M, Balbin O, Dhanasekaran S, Cao Q, Brenner J . Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol. 2011; 29(8):742-9. PMC: 3152676. DOI: 10.1038/nbt.1914. View

12.

Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin A, Kim S . The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 2012; 483(7391):603-7. PMC: 3320027. DOI: 10.1038/nature11003. View

13.

Prensner J, Chinnaiyan A . The emergence of lncRNAs in cancer biology. Cancer Discov. 2011; 1(5):391-407. PMC: 3215093. DOI: 10.1158/2159-8290.CD-11-0209. View

14.

Seo J, Ju Y, Lee W, Shin J, Lee J, Bleazard T . The transcriptional landscape and mutational profile of lung adenocarcinoma. Genome Res. 2012; 22(11):2109-19. PMC: 3483540. DOI: 10.1101/gr.145144.112. View

15.

Yang J, Li J, Jiang S, Zhou H, Qu L . ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. Nucleic Acids Res. 2012; 41(Database issue):D177-87. PMC: 3531181. DOI: 10.1093/nar/gks1060. View

16.

Chen G, Wang Z, Wang D, Qiu C, Liu M, Chen X . LncRNADisease: a database for long-non-coding RNA-associated diseases. Nucleic Acids Res. 2012; 41(Database issue):D983-6. PMC: 3531173. DOI: 10.1093/nar/gks1099. View

17.

Paraskevopoulou M, Georgakilas G, Kostoulas N, Reczko M, Maragkakis M, Dalamagas T . DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs. Nucleic Acids Res. 2012; 41(Database issue):D239-45. PMC: 3531175. DOI: 10.1093/nar/gks1246. View

18.

Kandoth C, Schultz N, Cherniack A, Akbani R, Liu Y, Shen H . Integrated genomic characterization of endometrial carcinoma. Nature. 2013; 497(7447):67-73. PMC: 3704730. DOI: 10.1038/nature12113. View

19.

Du Z, Fei T, Verhaak R, Su Z, Zhang Y, Brown M . Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nat Struct Mol Biol. 2013; 20(7):908-13. PMC: 3702647. DOI: 10.1038/nsmb.2591. View

20.

Bhartiya D, Pal K, Ghosh S, Kapoor S, Jalali S, Panwar B . lncRNome: a comprehensive knowledgebase of human long noncoding RNAs. Database (Oxford). 2013; 2013:bat034. PMC: 3708617. DOI: 10.1093/database/bat034. View