Comprehensive reconstruction and visualization of non-coding regulatory networks in human

Frontiers in Bioengineering and Biotechnology

Volumn 2, Issue DEC, 2014, Pages

  Bonnici, Vincenzo ^a   Russo, Francesco ^b,c   Bombieri, Nicola ^a   Pulvirenti, Alfredo ^d   Giugno, Rosalba ^d  

^a UNIVERSITY OF VERONA   (Italy)

^b INSTITUTE OF CLINICAL PHYSIOLOGY   (Italy)

^c UNIVERSITY OF PISA   (Italy)

^d UNIVERSITY OF CATANIA   (Italy)

Author keywords

Cytoscape; Gene expression; LncRNAs; MicroRNAs; Networks; Non coding RNAs

Indexed keywords

BODY FLUIDS; CODES (SYMBOLS); COMPLEX NETWORKS; ENZYME ACTIVITY; GENE EXPRESSION; NETWORKS (CIRCUITS); NUCLEIC ACIDS; RNA;

CYTOSCAPE; DATA INTERACTIONS; HUMAN BODY FLUIDS; LNCRNAS; MICRORNAS; NON-CODING RNAS; REGULATORY MECHANISM; REGULATORY NETWORK;

NETWORK CODING;

EID: 84934922535     PISSN: None     EISSN: 22964185     Source Type: Journal    
DOI: 10.3389/fbioe.2014.00069     Document Type: Article

References (54)

1. Amaral, P. P., Clark, M. B., Gascoigne, D. K., Dinger, M. E., and Mattick, J. S. (2011). lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res. 39(Suppl. 1), D146-D151. doi: 10.1093/nar/gkq1138
2. Attwooll, C., Oddi, S., Cartwright, P., Prosperini, E., Agger, K., Steensgaard, P., et al. (2005). A novel repressive E2F6 complex containing the polycomb group protein, EPC1, that interacts with EZH2 in a proliferation-specific manner. J Biol Chem 280, 1199-1208. doi:10.1074/jbc.M412509200
3. Batista, P. J., and Chang, H. Y. (2013). Long noncoding RNAs: cellular address codes in development and disease. Cell 152, 1298-1307. doi:10.1016/j.cell.2013.02.012
4. Betel, D., Wilson, M., Gabow, A., Marks, D. S., and Sander, C. (2008). The microRNA.org resource: targets and expression. Nucleic Acids Res. 36(Suppl. 1), D149-D153. doi:10.1093/nar/gkm995
5. Bu, D., Yu, K., Sun, S., Xie, C., Skogerbø, G., Miao, R., et al. (2011). NONCODE v3. 0: integrative annotation of long noncoding RNAs. Nucleic Acids Res. 40, D210-D215. doi:10.1093/nar/gkr1175
6. Cattell, R. (2011). Scalable SQL and NoSQL data stores. ACM SIGMOD Record 39, 12-27. doi:10.1145/1978915.1978919
7. Chen, G., Wang, Z., Wang, D., Qiu, C., Liu, M., Chen, X., et al. (2013). LncRNADisease: a database for long-non-coding RNA-associated diseases. Nucleic Acids Res. 41, D983-D986. doi:10.1093/nar/gks1099
8. Couzin, J. (2007). Erasing microRNAs reveals their powerful punch. Science 316, 5824. doi:10.1126/science.316.5824.530
9. ENCODE Project Consortium. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74. doi:10.1038/nature11247
10. Fatica, A., and Bozzoni, I. (2014). Long non-coding RNAs: new players in cell differentiation and development. Nat. Rev. Genet. 15, 7-21. doi:10.1038/nrg3606
11. Ferro, A., Giugno, R., Laganà, A., Mongioví, M., Pigola, G., Pulvirenti, A., et al. (2009). "miRScape: a cytoscape plugin to annotate biological networks with microRNAs," in Network Tools and Applications in Biology (NETTAB), Focused on Technologies, Tools and Applications for Collaborative and Social Bioinformatics Research and Development. ed. C. Romano (Catania: Libero di Scrivere).
12. Ghosal, S., Das, S., Sen, R., Basak, P., and Chakrabarti, J. (2013). Circ2Traits: a comprehensive database for circular RNA potentially associated with disease and traits. Front. Genet. 4:283. doi:10.3389/fgene.2013.00283
13. Gray, K. A., Daugherty, L. C., Gordon, S. M., Seal, R. L., Wright, M. W., and Bruford, E. A. (2012). Genenames.org: the HGNC resources in 2013. Nucleic Acids Res. 41, D545-D552. doi:10.1093/nar/gks1066
14. Guo, Z., Maki, M., Ding, R., Yang, Y., Zhang, B., and Xiong, L. (2014). Genome-wide survey of tissue-specific microRNA and transcription factor regulatory networks in 12 tissues. Sci. Rep. 4, 5150. doi:10.1038/srep05150
15. Gupta, R. A., Shah, N., Wang, K. C., Kim, J., Horlings, H. M., Wong, D. J., et al. (2010a). Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464, 1071-1076. doi:10.1038/nature08975
16. Gupta, S. K., Bang, C., and Thum, T. (2010b). Circulating microRNAs as biomarkers and potential paracrine mediators of cardiovascular disease. Circ. Cardiovasc. Genet. 3, 484-488. doi:10.1161/CIRCGENETICS.110.958363
17. Guttman, M., and Rinn, J. L. (2012). Modular regulatory principles of large non-coding RNAs. Nature 482, 339-346. doi:10.1038/nature10887
18. Han, J., Haihong, E., Le, G., and Du, J. (2011). Survey on NoSQL database. In Pervasive Computing and Applications (ICPCA). Port Elizabeth: IEEE, 363-366.
19. Hanke, M., Hoefig, K., Merz, H., Feller, A. C., Kausch, I., Jocham, D., et al. (2010). A robust methodology to study urine microRNA as tumor marker: microRNA-126 and microRNA-182 are related to urinary bladder cancer. Urol. Oncol. 28, 655-661. doi:10.1016/j.urolonc.2009.01.027
20. Hsu, S.-D., Tseng, Y.-T., Shrestha, S., Lin, Y.-L., Khaleel, A., Chou, C.-H., et al. (2014). miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic Acids Res. 42, D78-D85. doi:10.1093/nar/gkt1266
21. Huang, G., Athanassiou, C., and Benos, P. (2011). mirConnX: condition-specific mRNA-microRNA network integrator. Nucleic Acids Res. 39, W416-W423. doi:10.1093/nar/gkr276
22. Jeggari, A., Marks, D. S., and Larsson, E. (2012). miRcode: a map of putative microRNA target sites in the long non-coding transcriptome. Bioinformatics 28, 2062-2063. doi:10.1093/bioinformatics/bts344
23. Jiang, Q., Wang, Y., Hao, Y., Juan, L., Teng, M., Zhang, X., et al. (2009). miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res. 37(Suppl. 1), D98-D104. doi:10.1093/nar/gkn714
24. Kertesz, M., Iovino, N., Unnerstall, U., Gaul, U., and Segal, E. (2007). The role of site accessibility in microRNA target recognition. Nat. Genet. 39, 1278-1284. doi:10.1038/ng2135
25. Khalil, A. M., Guttman, M., Huarte, M., Garber, M., Raj, A., Morales, D. R., et al. (2009). Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. U.S.A. 106, 11667-11672. doi:10.1073/pnas.0904715106
26. Kogo, R., Shimamura, T., Mimori, K., Kawahara, K., Imoto, S., Sudo, T., et al. (2011). Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res. 71, 6320-6326. doi:10.1158/0008-5472.CAN-11-1021
27. Kozomara, A., and Griffiths-Jones, S. (2013). miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 42, D68-D73. doi:10.1093/nar/gkt1181
28. Krek, A., Grün, D., Poy, M. N., Wolf, R., Rosenberg, L., Epstein, E. J., et al. (2005). Combinatorial microRNA target predictions. Nat. Genet. 37, 495-500. doi:10.1038/ng1536
29. Kutmon, M., Kelde, T., Mandaviya, P., Evelo, C. T., and Coort, S. L. (2013). CyTargetLinker: a cytoscape app to integrate regulatory interactions in network analysis. PLoS ONE 8:e82160. doi:10.1371/journal.pone.0082160
30. Laczny, C., Leidinger, P., Haas, J., Ludwig, N., Backes, C., Gerasch, A., et al. (2012). miRTrail-a comprehensive webserver for analyzing gene and miRNA patterns to enhance the understanding of regulatory mechanisms in diseases. BMC Bioinformatics 13:36. doi:10.1186/1471-2105-13-36
31. Laganà, A., Forte, S., Giudice, A., Arena, M., Puglisi, P., Giugno, R., et al. (2009). miRò: a miRNA knowledge base. Database 2009, bap008. doi:10.1093/database/bap008
32. Le, T., Liu, L., Liu, B., Tsykin, A., Goodall, G., Satou, K., et al. (2013). Inferring microRNA and transcription factor regulatory networks in heterogeneous data. BMC Bioinformatics 14:92. doi:10.1186/1471-2105-14-92
33. Lewis, B. P., Burge, C. B., and Bartel, D. P. (2005). Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15-20. doi:10.1016/j.cell.2004.12.035
34. Li, J., Liu, S., Zhou, H., Qu, L., and Yang, J. (2014). starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 42, D92-D97. doi:10.1093/nar/gkt1248
35. Li, Y., Qiu, C., Tu, J., Geng, B., Yang, J., Jiang, T., et al. (2013). HMDD v2. 0: a database for experimentally supported human microRNA and disease associations. Nucleic Acids Res. 42, D1070-D1074. doi:10.1093/nar/gkt1023
36. Liu, B., Li, J., Tsykin, A., Liu, L., Gaur, A., and Goodall, G. (2009). Exploring complex miRNA-mRNA interactions with Bayesian networks by splitting averaging strategy. BMC Bioinformatics 10:408. doi:10.1186/1471-2105-10-408
37. Liu, Z.-P., Wu, H., Zhu, J., and Miao, H. (2014). Systematic identification of transcriptional and post-transcriptional regulations in human respiratory epithelial cells during influenza A virus infection. BMC Bioinformatics 15:336. doi:10.1186/1471-2105-15-336
38. Loher, P., and Rigoutsos, I. (2012). Interactive exploration of RNA22 microRNA target predictions. Bioinformatics 28, 3322-3323. doi:10.1093/bioinformatics/bts615
39. Lu, J., Getz, G., Miska, E. A., Alvarez-Saavedra, E., Lamb, J., Peck, D., et al. (2005). MicroRNA expression profiles classify human cancers. Nature 435, 834-838. doi:10.1038/nature03702
40. Margueron, R., Li, G., Sarma, K., Blais, A., Zavadil, J., Woodcock, C. L., et al. (2008). Ezh1 and Ezh2 maintain repressive chromatin through different mechanisms. Mol. Cell 32, 503-518. doi:10.1016/j.molcel.2008.11.004
41. Mattick, J. S. (2001). Non-coding RNAs: the architects of eukaryotic complexity. EMBO Rep. 2, 986-991. doi:10.1093/embo-reports/kve230
42. Memczak, S., Jens, M., Elefsinioti, A., Torti, F., Krueger, J., Rybak, A., et al. (2013). Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495, 333-338. doi:10.1038/nature11928
43. Mitchell, P. S., Parkin, R. K., Kroh, E. M., Fritz, B. R., Wyman, S. K., Pogosova-Agadjanyan, E. L., et al. (2008). Circulating microRNAs as stable blood-based markers for cancer detection. Proc. Natl. Acad. Sci.U.S.A. 105, 10513-10518. doi:10.1073/pnas.0804549105
44. Rinn, J. L., and Chang, H. Y. (2012). Genome regulation by long noncoding RNAs. Annu. Rev. Biochem. 81, 145-166. doi:10.1146/annurev-biochem-051410-092902
45. Russo, F., Di Bella, S., Bonnici, V., Laganà, A., Rainaldi, G., Pellegrini, M., et al. (2014). A knowledge base for the discovery of function, diagnostic potential and drug effects on cellular and extracellular miRNAs. BMC Genomics 15:1-7. doi:10.1186/1471-2164-15-S3-S4
46. Russo, F., Di Bella, S., Nigita, G., Macca, V., Lagana, A., Giugno, R., et al. (2012). miRandola: extracellular circulating microRNAs database. PLoS ONE 7:e47786. doi:10.1371/journal.pone.0047786
47. Sales, G., Coppe, A., Bisognin, A., Biasiolo, M., Bortoluzzi, S., and Romualdi, C. (2010). MAGIA, a web-based tool for miRNA and genes integrated analysis. Nucleic Acids Res. 38, W352-W359. doi:10.1093/nar/gkq423
48. Shannon, P., Markiel, A., Ozier, O., Baliga, N., Wang, J., Ramage, D., et al. (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504. doi:10.1101/gr.1239303
49. Song, Y., Xu, Y., Wang, Z., Chen, Y., Yue, Z., Gao, P., et al. (2012). MicroRNA-148b suppresses cell growth by targeting cholecystokinin-2 receptor in colorectal cancer. Int. J. Cancer 131, 1042-1051. doi:10.1002/ijc.26485
50. Stonebraker, M. (2010). SQL databases v. NoSQL databases. Commun. ACM 53, 10-11. doi:10.1145/1721654.1721659
51. Tay, Y., Kats, L., Salmena, L., Weiss, D., Tan, S. M., Ala, U., et al. (2011). Coding-independent regulation of the tumor suppressor PTEN by competing endogenous MRNAs. Cell 147, 344-357. doi:10.1016/j.cell.2011.09.029
52. Tesoriero, C. (2013). Getting Started with OrientDB. Birmingham: Packt Publishing Ltd.
53. UniProt Consortium. (2013). Update on activities at the universal protein resource (UniProt) in 2013. Nucleic Acids Res. 41, D43-D47. doi:10.1093/nar/gks1068
54. Wu, T., Wang, J., Liu, C., Zhang, Y., Shi, B., Zhu, X., et al. (2006). NPInter: the noncoding RNAs and protein related biomacromolecules interaction database. Nucleic Acids Res. 34(Suppl. 1), D150-D152. doi:10.1093/nar/gkj025