TSGene 2.0: An updated literature-based knowledgebase for Tumor Suppressor Genes

Nucleic Acids Research

Volumn 44, Issue D1, 2016, Pages D1023-D1031

  Zhao, Min ^a   Kim, Pora ^b   Mitra, Ramkrishna ^b   Zhao, Junfei ^b   Zhao, Zhongming ^b,c,d  

^a UNIVERSITY OF THE SUNSHINE COAST   (Australia)

^b VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

^c VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d UNIVERSITY OF TEXAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DOWN REGULATION; GENE EXPRESSION; GENE MUTATION; GENE SEQUENCE; GENETIC DATABASE; GENETIC SCREENING; HUMAN; PRIORITY JOURNAL; TUMOR SUPPRESSOR GENE; GENE EXPRESSION REGULATION; GENETICS; KNOWLEDGE BASE; MEDLINE; MOLECULAR GENETICS; MUTATION; NEOPLASM; NUCLEIC ACID DATABASE;

LONG UNTRANSLATED RNA; MICRORNA; TUMOR SUPPRESSOR PROTEIN;

DATABASES, NUCLEIC ACID; DOWN-REGULATION; GENE EXPRESSION REGULATION, NEOPLASTIC; GENES, TUMOR SUPPRESSOR; HUMANS; KNOWLEDGE BASES; MICRORNAS; MOLECULAR SEQUENCE ANNOTATION; MUTATION; NEOPLASMS; PUBMED; RNA, LONG NONCODING; TUMOR SUPPRESSOR PROTEINS;

EID: 84976898464     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv1268     Document Type: Article

References (66)

1. Siegel, R. L., Miller, K. D. and Jemal, A. (2015) Cancer statistics, 2015. CA Cancer J. Clin., 65, 5-29.
2. Balmain, A., Gray, J. and Ponder, B. (2003) The genetics and genomics of cancer. Nat. Genet., 33(Suppl), 238-244.
3. Haber, D. A. and Settleman, J. (2007) Cancer: drivers and passengers. Nature, 446, 145-146.
4. Esteller, M. (2002) CpG island hypermethylation and tumor suppressor genes: a booming present, a brighter future. Oncogene, 21, 5427-5440.
5. Zack, T. I., Schumacher, S. E., Carter, S. L., Cherniack, A. D., Saksena, G., Tabak, B., Lawrence, M. S., Zhsng, C. Z., Wala, J., Mermel, C. H. et al. (2013) Pan-cancer patterns of somatic copy number alteration. Nat. Genet., 45, 1134-1140.
6. Mavrakis, K. J., Van Der Meulen, J., Wolfe, A. L., Liu, X., Mets, E., Taghon, T., Khan, A. A., Setty, M., Rondou, P., Vandenberghe, P. et al. (2011) A cooperative microRNA-tumor suppressor gene network in acute T-cell lymphoblastic leukemia (T-ALL). Nat. Genet., 43, 673-678.
7. Tay, Y., Kats, L., Salmena, L., Weiss, D., Tan, S. M., Ala, U., Karreth, F., Poliseno, L., Provero, P., Di Cunto, F. et al. (2011) Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell, 147, 344-357.
8. Sherr, C. J. (2004) Principles of tumor suppression. Cell, 116, 235-246.
9. Chen, C. Z. (2005) MicroRNAs as oncogenes and tumor suppressors. New Engl. J. Med., 353, 1768-1771.
10. Hammond, S. M. (2007) MicroRNAs as tumor suppressors. Nat. Genet., 39, 582-583.
11. Zhang, B. H., Pan, X. P., Cobb, G. P. and Anderson, T. A. (2007) microRNAs as oncogenes and tumor suppressors. Dev. Biol., 302, 1-12.
12. Prensner, J. R. and Chinnaiyan, A. M. (2011) The emergence of lncRNAs in cancer biology. Cancer Discov., 1, 391-407.
13. Zhao, M., Sun, J. and Zhao, Z. (2013) TSGene: a web resource for tumor suppressor genes. Nucleic Acids Res., 41, D970-D976.
14. Crystal, A. S., Shaw, A. T., Sequist, L. V., Friboulet, L., Niederst, M. J., Lockerman, E. L., Frias, R. L., Gainor, J. F., Amzallag, A., Greninger, P. et al. (2014) Patient-derived models of acquired resistance can identify effective drug combinations for cancer. Science, 346, 1480-1486.
15. Wagner, T. A., McLaughlin, S., Garg, K., Cheung, C. Y., Larsen, B. B., Styrchak, S., Huang, H. C., Edlefsen, P. T., Mullins, J. I. and Frenkel, L. M. (2014) HIV latency. Proliferation of cells with HIV integrated into cancer genes contributes to persistent infection. Science, 345, 570-573.
16. Cohn, L. B., Silva, I. T., Oliveira, T. Y., Rosales, R. A., Parrish, E. H., Learn, G. H., Hahn, B. H., Czartoski, J. L., McElrath, M. J., Lehmann, C. et al. (2015) HIV-1 integration landscape during latent and active infection. Cell, 160, 420-432.
17. AlQuraishi, M., Koytiger, G., Jenney, A., MacBeath, G. and Sorger, P. K. (2014) A multiscale statistical mechanical framework integrates biophysical and genomic data to assemble cancer networks. Nat. Genet., 46, 1363-1371.
18. Yoshihara, K., Wang, Q., Torres-Garcia, W., Zheng, S., Vegesna, R., Kim, H. and Verhaak, R. G. (2015) The landscape and therapeutic relevance of cancer-associated transcript fusions. Oncogene, 34, 4845-4854.
19. Blattler, A., Yao, L., Witt, H., Guo, Y., Nicolet, C. M., Berman, B. P. and Farnham, P. J. (2014) Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes. Genome Biol., 15, 469-484.
20. Gilbert, L. A., Horlbeck, M. A., Adamson, B., Villalta, J. E., Chen, Y., Whitehead, E. H., Guimaraes, C., Panning, B., Ploegh, H. L., Bassik, M. C. et al. (2014) Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation. Cell, 159, 647-661.
21. Liu, H., Flores, M. A., Meng, J., Zhang, L., Zhao, X., Rao, M. K., Chen, Y. and Huang, Y. (2015) MeT-DB: a database of transcriptome methylation in mammalian cells. Nucleic Acids Res., 43, D197-D203.
22. Zhao, M., Sun, J. and Zhao, Z. (2012) Distinct and competitive regulatory patterns of tumor suppressor genes and oncogenes in ovarian cancer. PLoS One, 7, e44175.
23. Zhao, M., Sun, J. and Zhao, Z. (2013) Synergetic regulatory networks mediated by oncogene-driven microRNAs and transcription factors in serous ovarian cancer. Mol. Biosyst., 9, 3187-3198.
24. Zhao, M. and Zhao, Z. (2013) CNVannotator: a comprehensive annotation server for copy number variation in the human genome. PLoS One, 8, e80170.
25. Lu, Z., Cohen, K. B. and Hunter, L. (2007) GeneRIF quality assurance as summary revision. Pac. Symp. Biocomput., 2007, 269-280.
26. Santoro, F., Botrugno, O. A., Dal Zuffo, R., Pallavicini, I., Matthews, G. M., Cluse, L., Barozzi, I., Senese, S., Fornasari, L., Moretti, S. et al. (2013) A dual role for Hdac1: oncosuppressor in tumorigenesis, oncogene in tumor maintenance. Blood, 121, 3459-3468.
27. Pelosi, G., Fumagalli, C., Trubia, M., Sonzogni, A., Rekhtman, N., Maisonneuve, P., Galetta, D., Spaggiari, L., Veronesi, G., Scarpa, A. et al. (2010) Dual role of RASSF1 as a tumor suppressor and an oncogene in neuroendocrine tumors of the lung. Anticancer Res., 30, 4269-4281.
28. Lobry, C., Oh, P. and Aifantis, I. (2011) Oncogenic and tumor suppressor functions of Notch in cancer: it's NOTCH what you think. J. Exp. Med., 208, 1931-1935.
29. Lamouille, S. and Derynck, R. (2009) Oncogene and tumour suppressor: the two faces of SnoN. EMBO J., 28, 3459-3460.
30. Yang, L., Han, Y., Suarez Saiz, F. and Minden, M. D. (2007) A tumor suppressor and oncogene: the WT1 story. Leukemia, 21, 868-876.
31. Uribesalgo, I., Benitah, S. A. and Di Croce, L. (2012) From oncogene to tumor suppressor: the dual role of Myc in leukemia. Cell Cycle, 11, 1757-1764.
32. Vogelstein, B., Papadopoulos, N., Velculescu, V. E., Zhou, S., Diaz, L. A. Jr and Kinzler, K. W. (2013) Cancer genome landscapes. Science, 339, 1546-1558.
33. Wang, D., Qiu, C., Zhang, H., Wang, J., Cui, Q. and Yin, Y. (2010) Human microRNA oncogenes and tumor suppressors show significantly different biological patterns: from functions to targets. PLoS One, 5, e13067.
34. Cerami, E. G., Gross, B. E., Demir, E., Rodchenkov, I., Babur, O., Anwar, N., Schultz, N., Bader, G. D. and Sander, C. (2011) Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res., 39, D685-D690.
35. Vitale, N., Horiba, K., Ferrans, V. J., Moss, J. and Vaughan, M. (1998) Localization of ADP-ribosylation factor domain protein 1 (ARD1) in lysosomes and Golgi apparatus. Proc. Natl. Acad. Sci. U. S. A., 95, 8613-8618.
36. Chen, J., Bardes, E. E., Aronow, B. J. and Jegga, A. G. (2009) ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res., 37, W305-W311.
37. Vlachos, I. S., Zagganas, K., Paraskevopoulou, M. D., Georgakilas, G., Karagkouni, D., Vergoulis, T., Dalamagas, T. and Hatzigeorgiou, A. G. (2015) DIANA-miRPath v3.0: deciphering microRNA function with experimental support. Nucleic Acids Res., 43, W460-W466.
38. O'Day, E. and Lal, A. (2010) MicroRNAs and their target gene networks in breast cancer. Breast Cancer Res., 12, 201.
39. Hua, D., Ding, D., Han, X., Zhang, W., Zhao, N., Foltz, G., Lan, Q., Huang, Q. and Lin, B. (2012) Human miR-31 targets radixin and inhibits migration and invasion of glioma cells. Oncol. Rep., 27, 700-706.
40. Kent, O. A. and Mendell, J. T. (2006) A small piece in the cancer puzzle: microRNAs as tumor suppressors and oncogenes. Oncogene, 25, 6188-6196.
41. Yu, J., Wu, W. K., Li, X., He, J., Li, X. X., Ng, S. S., Yu, C., Gao, Z., Yang, J., Li, M. et al. (2015) Novel recurrently mutated genes and a prognostic mutation signature in colorectal cancer. Gut, 64, 636-645.
42. Davoli, T., Xu, A. W., Mengwasser, K. E., Sack, L. M., Yoon, J. C., Park, P. J. and Elledge, S. J. (2013) Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome. Cell, 155, 948-962.
43. NCBI Resource Coordinators. (2015) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 43, D6-D17.
44. Zhao, M., Li, Z. and Qu, H. (2015) An evidence-based knowledgebase of metastasis suppressors to identify key pathways relevant to cancer metastasis. Sci. Rep., 5, 15478.
45. Gao, J., Aksoy, B. A., Dogrusoz, U., Dresdner, G., Gross, B., Sumer, S. O., Sun, Y., Jacobsen, A., Sinha, R., Larsson, E. et al. (2013) Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci. Signal., 6, pl1.
46. Yao, J., Zhou, B., Zhang, J., Geng, P., Liu, K., Zhu, Y. and Zhu, W. (2014) A new tumor suppressor LncRNA ADAMTS9-AS2 is regulated by DNMT1 and inhibits migration of glioma cells. Tumour Biol., 35, 7935-7944.
47. Wang, P., Liu, Y. H., Yao, Y. L., Li, Z., Li, Z. Q., Ma, J. and Xue, Y. X. (2015) Long non-coding RNA CASC2 suppresses malignancy in human gliomas by miR-21. Cell. Signal., 27, 275-282.
48. Baldinu, P., Cossu, A., Manca, A., Satta, M. P., Sini, M. C., Palomba, G., Dessole, S., Cherchi, P., Mara, L., Tanda, F. et al. (2007) CASC2a gene is down-regulated in endometrial cancer. Anticancer Res., 27, 235-243.
49. Liu, Y., Corcoran, M., Rasool, O., Ivanova, G., Ibbotson, R., Grander, D., Iyengar, A., Baranova, A., Kashuba, V., Merup, M. et al. (1997) Cloning of two candidate tumor suppressor genes within a 10 kb region on chromosome 13q14, frequently deleted in chronic lymphocytic leukemia. Oncogene, 15, 2463-2473.
50. Bullrich, F., Fujii, H., Calin, G., Mabuchi, H., Negrini, M., Pekarsky, Y., Rassenti, L., Alder, H., Reed, J. C., Keating, M. J. et al. (2001) Characterization of the 13q14 tumor suppressor locus in CLL: identification of ALT1, an alternative splice variant of the LEU2 gene. Cancer Res., 61, 6640-6648.
51. Xia, T., Chen, S., Jiang, Z., Shao, Y., Jiang, X., Li, P., Xiao, B. and Guo, J. (2015) Long noncoding RNA FER1L4 suppresses cancer cell growth by acting as a competing endogenous RNA and regulating PTEN expression. Sci. Rep., 5, 13445.
52. Mourtada-Maarabouni, M., Pickard, M. R., Hedge, V. L., Farzaneh, F. and Williams, G. T. (2009) GAS5, a non-protein-coding RNA, controls apoptosis and is downregulated in breast cancer. Oncogene, 28, 195-208.
53. Hao, Y., Crenshaw, T., Moulton, T., Newcomb, E. and Tycko, B. (1993) Tumour-suppressor activity of H19 RNA. Nature, 365, 764-767.
54. Marin-Bejar, O., Marchese, F. P., Athie, A., Sanchez, Y., Gonzalez, J., Segura, V., Huang, L., Moreno, I., Navarro, A., Monzo, M. et al. (2013) Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2. Genome Biol., 14, R104.
55. Gong, Z., Zhang, S., Zeng, Z., Wu, H., Yang, Q., Xiong, F., Shi, L., Yang, J., Zhang, W., Zhou, Y. et al. (2014) LOC401317, a p53-regulated long non-coding RNA, inhibits cell proliferation and induces apoptosis in the nasopharyngeal carcinoma cell line HNE2. PLoS One, 9, e110674.
56. Yu, W., Qiao, Y., Tang, X., Ma, L., Wang, Y., Zhang, X., Weng, W., Pan, Q., Yu, Y., Sun, F. et al. (2014) Tumor suppressor long non-coding RNA, MT1DP is negatively regulated by YAP and Runx2 to inhibit FoxA1 in liver cancer cells. Cell. Signal., 26, 2961-2968.
57. Fan, M., Li, X., Jiang, W., Huang, Y., Li, J. and Wang, Z. (2013) A long non-coding RNA, PTCSC3, as a tumor suppressor and a target of miRNAs in thyroid cancer cells. Exp. Ther. Med., 5, 1143-1146.
58. Chen, C. L., Tseng, Y. W., Wu, J. C., Chen, G. Y., Lin, K. C., Hwang, S. M. and Hu, Y. C. (2015) Suppression of hepatocellular carcinoma by baculovirus-mediated expression of long non-coding RNA PTENP1 and MicroRNA regulation. Biomaterials, 44, 71-81.
59. Zapata-Benavides, P., Mendez-Vazquez, J. L., Gonzalez-Rocha, T. R., Zamora-Avila, D. E., Franco-Molina, M. A., Garza-Garza, R. and Rodriguez-Padilla, C. (2009) Expression of prostate apoptosis response (Par-4) is associated with progesterone receptor in breast cancer. Arch. Med. Res., 40, 595-599.
60. Chen, H. Y., Wen, J. M., Xiao, X. W., Li, D. J., Guo, X. L., Long, Z., Dai, Y. B. and Tang, Y. X. (2010) Expression of human testis development related gene 1 in testicular cancer detected by tissue microarray. Zhonghua Nan Ke Xue, 16, 883-886.
61. Huarte, M., Guttman, M., Feldser, D., Garber, M., Koziol, M. J., Kenzelmann-Broz, D., Khalil, A. M., Zuk, O., Amit, I., Rabani, M. et al. (2010) A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell, 142, 409-419.
62. Liu, Q., Huang, J., Zhou, N., Zhang, Z., Zhang, A., Lu, Z., Wu, F. and Mo, Y. Y. (2013) LncRNA loc285194 is a p53-regulated tumor suppressor. Nucleic Acids Res., 41, 4976-4987.
63. Pasic, I., Shlien, A., Durbin, A. D., Stavropoulos, D. J., Baskin, B., Ray, P. N., Novokmet, A. and Malkin, D. (2010) Recurrent focal copy-number changes and loss of heterozygosity implicate two noncoding RNAs and one tumor suppressor gene at chromosome 3q13.31 in osteosarcoma. Cancer Res., 70, 160-171.
64. Yildirim, E., Kirby, J. E., Brown, D. E., Mercier, F. E., Sadreyev, R. I., Scadden, D. T. and Lee, J. T. (2013) Xist RNA is a potent suppressor of hematologic cancer in mice. Cell, 152, 727-742.
65. Askarian-Amiri, M. E., Crawford, J., French, J. D., Smart, C. E., Smith, M. A., Clark, M. B., Ru, K., Mercer, T. R., Thompson, E. R., Lakhani, S. R. et al. (2011) SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer. RNA, 17, 878-891.
66. Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B Stat. Methodol., 57, 289-300.