Long non-coding RNAs function annotation: A global prediction method based on bi-colored networks

Nucleic Acids Research

Volumn 41, Issue 2, 2013, Pages

  Guo, Xingli ^a,b   Gao, Lin ^a   Liao, Qi ^b,c   Xiao, Hui ^b   Ma, Xiaoke ^a   Yang, Xiaofei ^a   Luo, Haitao ^b   Zhao, Guoguang ^b,d   Bu, Dechao ^b,d   Jiao, Fei ^e   Shao, Qixiang ^f   Chen, Run Sheng ^g   Zhao, Yi ^b  

^a XIDIAN UNIVERSITY   (China)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^c NINGBO UNIVERSITY   (China)

^d UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^e BINZHOU MEDICAL UNIVERSITY   (China)

^f JIANGSU UNIVERSITY   (China)

^g INSTITUTE OF BIOPHYSICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

LONG UNTRANSLATED RNA;

ACCURACY; ANALYTIC METHOD; ANIMAL CELL; ARTICLE; BRAIN REGION; CALCULATION; CELL ADHESION; CELL DEATH; CELL DIFFERENTIATION; CONTROLLED STUDY; EMBRYO; EMBRYO CELL; GENE EXPRESSION; GENE FUNCTION; INTERMETHOD COMPARISON; LONG NON CODING RNA GLOBAL FUNCTION PREDICTOR; MITOSIS; MOUSE; NERVE CELL; NERVOUS SYSTEM DEVELOPMENT; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; STEM CELL;

ALGORITHMS; ANIMALS; BRAIN; EMBRYONIC STEM CELLS; GENE EXPRESSION; HUMANS; MICE; MOLECULAR SEQUENCE ANNOTATION; NEURONS; PROTEIN INTERACTION MAPS; RNA, LONG UNTRANSLATED;

EID: 84875417100     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks967     Document Type: Article

References (61)

1. Okazaki, Y., Furuno, M., Kasukawa, T., Adachi, J., Bono, H., Kondo, S., Nikaido, I., Osato, N., Saito, R., Suzuki, H. et al. (2002) Analysis of the mouse transcriptome based on functional annotation of 60, 770 full-length cDNAs. Nature, 420, 563-573. (Pubitemid 35477049)
2. Ota, T., Suzuki, Y., Nishikawa, T., Otsuki, T., Sugiyama, T., Irie, R., Wakamatsu, A., Hayashi, K., Sato, H., Nagai, K. et al. (2003) Complete sequencing and characterization of 21, 243 full-length human cDNAs. Nat. Genet., 36, 40-45.
3. Tupy, J.L., Bailey, A.M., Dailey, G., Evans-Holm, M., Siebel, C.W., Misra, S., Celniker, S.E. and Rubin, G.M. (2005) Identification of putative noncoding polyadenylated transcripts in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA, 102, 5495-5500. (Pubitemid 40530286)
4. Guttman, M., Amit, I., Garber, M., French, C., Lin, M.F., Feldser, D., Huarte, M., Zuk, O., Carey, B.W., Cassady, J.P. et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 458, 223-227.
5. Guttman, M., Garber, M., Levin, J.Z., Donaghey, J., Robinson, J., Adiconis, X., Fan, L., Koziol, M.J., Gnirke, A., Nusbaum, C. et al. (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol., 28, 503-510.
6. Cabili, M.N., Trapnell, C., Goff, L., Koziol, M., Tazon-Vega, B., Regev, A. and Rinn, J.L. (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev., 25, 1915-1927.
7. Kim, T.K., Hemberg, M., Gray, J.M., Costa, A.M., Bear, D.M., Wu, J., Harmin, D.A., Laptewicz, M., Barbara-Haley, K., Kuersten, S. et al. (2010) Widespread transcription at neuronal activity-regulated enhancers. Nature, 465, 182-187.
8. Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. and Wold, B. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods, 5, 621-628. (Pubitemid 351911867)
9. Taft, R.J., Pang, K.C., Mercer, T.R., Dinger, M. and Mattick, J.S. (2010) Non-coding RNAs: regulators of disease. J. Pathol., 220, 126-139.
10. Wilusz, J.E., Sunwoo, H. and Spector, D.L. (2009) Long noncoding RNAs: functional surprises from the RNA world. Genes Dev., 23, 1494-1504.
11. Mercer, T.R., Dinger, M.E. and Mattick, J.S. (2009) Long non-coding RNAs: insights into functions. Nat. Rev. Genet., 10, 155-159.
12. Gibb, E.A., Brown, C.J. and Lam, W.L. (2011) The functional role of long non-coding RNA in human carcinomas. Mol. Cancer, 10, 38.
13. Koerner, M.V., Pauler, F.M., Huang, R. and Barlow, D.P. (2009) The function of non-coding RNAs in genomic imprinting. Development, 136, 1771-1783.
14. Clark, M.B., Johnston, R.L., Inostroza-Ponta, M., Fox, A.H., Fortini, E., Moscato, P., Dinger, M.E. and Mattick, J.S. (2012) Genome-wide analysis of long noncoding RNA stability. Genome Res., 22, 885-898.
15. Guttman, M. and Rinn, J.L. (2012) Modular regulatory principles of large non-coding RNAs. Nature, 482, 339-346.
16. Wapinski, O. and Chang, H.Y. (2011) Long noncoding RNAs and human disease. Trends Cell Biol., 21, 354-361.
17. Pang, K.C., Frith, M.C. and Mattick, J.S. (2006) Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. Trends Genet., 22, 1-5. (Pubitemid 43011990)
18. Pang, K.C., Dinger, M.E., Mercer, T.R., Malquori, L., Grimmond, S.M., Chen, W. and Mattick, J.S. (2009) Genome-wide identification of long noncoding RNAs in CD8+T cells. J. Immunol., 182, 7738-7748.
19. Khalil, A.M., Guttman, M., Huarte, M., Garber, M., Raj, A., Rivea Morales, D., Thomas, K., Presser, A., Bernstein, B.E., Van Oudenaarden, A. et al. (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. USA, 106, 11667-11672.
20. Liao, Q., Liu, C., Yuan, X., Kang, S., Miao, R., Xiao, H., Zhao, G., Luo, H., Bu, D., Zhao, H. et al. (2011) Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network. Nucleic Acids Res., 39, 3864-3878.
21. Sharan, R., Ulitsky, I. and Shamir, R. (2007) Network-based prediction of protein function. Mol. Syst. Biol., 3, 88.
22. Von Mering, C., Jensen, L.J., Snel, B., Hooper, S.D., Krupp, M., Foglierini, M., Jouffre, N., Huynen, M.A. and Bork, P. (2005) STRING: known and predicted proteinprotein associations, integrated and transferred across organisms. Nucleic acids research, 33(Suppl 1), D433-D437. (Pubitemid 40207910)
23. Lee, H.K., Hsu, A.K., Sajdak, J., Qin, J. and Pavlidis, P. (2004) Coexpression analysis of human genes across many microarray data sets. Genome Res., 14, 1085-1094. (Pubitemid 38811545)
24. Eisen, M.B., Spellman, P.T., Brown, P.O. and Botstein, D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA, 95, 14863-14868. (Pubitemid 29003722)
25. Pruitt, K.D., Tatusova, T., Klimke, W. and Maglott, D.R. (2009) NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res., 37, D32-D36.
26. Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C. et al. (2005) The transcriptional landscape of the mammalian genome. Science, 309, 1559-1563.
27. Jensen, L.J., Kuhn, M., Stark, M., Chaffron, S., Creevey, C., Muller, J., Doerks, T., Julien, P., Roth, A., Simonovic, M. et al. (2009) STRING 8- A global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res., 37, D412-D416.
28. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T. et al. (2000) Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29. (Pubitemid 30257031)
29. Zhou, D., Bousquet, O., Lal, T.N., Weston, J. and Scholkopf, B. (2004) Learning with local and global consistency. Adv. Neural Inf. Process. Syst., 16, 321-328.
30. Vanunu, O., Magger, O., Ruppin, E., Shlomi, T. and Sharan, R. (2010) Associating genes and protein complexes with disease via network propagation. PLoS Comput. Biol., 6, e1000641.
31. Zhu, X. and Goldberg, A.B. (2009) Introduction to semi-supervised learning. Synth. Lect. Artif. Intell. Mach. Learn., 3, 1-130.
32. Jebara, T., Wang, J., Chang, S.F. and Proceedings of the 26th Annual International Conference on Machine Learning (2009) Graph construction and b-matching for semi-supervised learning, pp. 441-448.
33. Deng, M., Zhang, K., Mehta, S., Chen, T. and Sun, F. (2003) Prediction of protein function using protein-protein interaction data. J. Comput. Biol., 10, 947-960. (Pubitemid 38156407)
34. Hishigaki, H., Nakai, K., Ono, T., Tanigami, A. and Takagi, T. (2001) Assessment of prediction accuracy of protein function from protein-protein interaction data. Yeast, 18, 523-531. (Pubitemid 32318334)
35. Chua, H.N., Sung, W.K. and Wong, L. (2006) Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. Bioinformatics, 22, 1623-1630. (Pubitemid 43985296)
36. Nabieva, E., Jim, K., Agarwal, A., Chazelle, B. and Singh, M. (2005) Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. Bioinformatics, 21, i302-i310. (Pubitemid 41794502)
37. Schwikowski, B., Uetz, P. and Fields, S. (2000) A network of proteinprotein interactions in yeast. Nat. Biotechnol., 18, 1257-1261.
38. Chang, H.Y. and Rinn, J.L. (2012) Genome regulation by long noncoding RNAs. Annu. Rev. Biochem., 81, 145-166.
39. Dinger, M.E., Amaral, P.P., Mercer, T.R., Pang, K.C., Bruce, S.J., Gardiner, B.B., Askarian-Amiri, M.E., Ru, K., Soldà , G., Simons, C. et al. (2008) Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res., 18, 1433-1445.
40. Lee, I., Ambaru, B., Thakkar, P., Marcotte, E.M. and Rhee, S.Y. (2010) Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nat. Biotechnol., 28, 149-156.
41. Cui, Q., Ma, Y., Jaramillo, M., Bari, H., Awan, A., Yang, S., Zhang, S., Liu, L., Lu, M., O'Connor-McCourt, M. et al. (2007) A map of human cancer signaling. Mol. Syst. Biol., 3, 152.
42. Cui, Q., Yu, Z., Purisima, E.O. and Wang, E. (2006) Principles of microRNA regulation of a human cellular signaling network. Mol. Syst. Biol., 2, 46.
43. Kanehisa, M., Goto, S., Sato, Y., Furumichi, M. and Tanabe, M. (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res., 40, D109-D114.
44. Amaral, P.P. and Mattick, J.S. (2008) Noncoding RNA in development. Mamm. Genome, 19, 454-492.
45. Guttman, M., Donaghey, J., Carey, B.W., Garber, M., Grenier, J.K., Munson, G., Young, G., Lucas, A.B., Ach, R., Bruhn, L. et al. (2011) lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature, 477, 295-300.
46. Mohamed, J.S., Gaughwin, P.M., Lim, B., Robson, P. and Lipovich, L. (2010) Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells. RNA, 16, 324-337.
47. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402. (Pubitemid 27359211)
48. Blackshaw, S., Harpavat, S., Trimarchi, J., Cai, L., Huang, H., Kuo, W.P., Weber, G., Lee, K., Fraioli, R.E., Cho, S.H. et al. (2004) Genomic analysis of mouse retinal development. PLoS Biol., 2, e247.
49. Chodroff, R.A., Goodstadt, L., Sirey, T.M., Oliver, P.L., Davies, K.E., Green, E.D., Molnar, Z. and Ponting, C.P. (2010) Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes. Genome Biol., 11, R72.
50. Mercer, T.R., Dinger, M.E., Sunkin, S.M., Mehler, M.F. and Mattick, J.S. (2008) Specific expression of long noncoding RNAs in the mouse brain. Proc. Natl. Acad. Sci. USA, 105, 716-721. (Pubitemid 351171774)
51. Mercer, T.R., Qureshi, I.A., Gokhan, S., Dinger, M.E., Li, G., Mattick, J.S. and Mehler, M.F. (2010) Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation. BMC Neurosci., 11, 14.
52. Tripathi, V., Ellis, J.D., Shen, Z., Song, D.Y., Pan, Q., Watt, A.T., Freier, S.M., Bennett, C.F., Sharma, A., Bubulya, P.A. et al. (2010) The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol. Cell, 39, 925-938.
53. Bellucci, M., Agostini, F., Masin, M. and Tartaglia, G.G. (2011) Predicting protein associations with long noncoding RNAs. Nat. Methods, 8, 444-445.
54. Khalil, A.M. and Rinn, J.L. (2011) RNA-protein interactions in human health and disease. Semin. Cell Dev. Biol., 22, 359-365.
55. Gupta, R.A., Shah, N., Wang, K.C., Kim, J., Horlings, H.M., Wong, D.J., Tsai, M.C., Hung, T., Argani, P., Rinn, J.L. et al. (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature, 464, 1071-1076.
56. Wu, L.F., Hughes, T.R., Davierwala, A.P., Robinson, M.D., Stoughton, R. and Altschuler, S.J. (2002) Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nat. Genet., 31, 255-265.
57. Pellissier, F., Gerber, A., Bauer, C., Ballivet, M. and Ossipow, V. (2007) The adhesion molecule Necl-3/SynCAM-2 localizes to myelinated axons, binds to oligodendrocytes and promotes cell adhesion. BMC Neurosci., 8, 90.
58. Sun, Y., Da Costa, N. and Chang, K. (2003) Cluster characterisation and temporal expression of porcine sarcomeric myosin heavy chain genes. J. Muscle Res. Cell Motil., 24, 561-570. (Pubitemid 38141882)
59. Ponjavic, J., Oliver, P.L., Lunter, G. and Ponting, C.P. (2009) Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain. PLoS Genet., 5, e1000617.
60. Makarova, J.A. and Kramerov, D.A. (2005) Noncoding RNA of U87 host gene is associated with ribosomes and is relatively resistant to nonsense-mediated decay. Gene, 363, 51-60. (Pubitemid 41691892)
61. Dong, B., Zhang, P., Chen, X., Liu, L., Wang, Y., He, S. and Chen, R. (2011) Predicting housekeeping genes based on Fourier analysis. PloS One, 6, e21012.