Analysis of expression on human chromosome 21, ALE-HSA21: A pilot integrated web resource

Database

Volumn 2014, Issue , 2014, Pages

  Scarpato, Margherita ^a   Esposito, Roberta ^a,b   Evangelista, Daniela ^c,d   Aprile, Marianna ^a   Ambrosio, Maria Rosaria ^a   Angelini, Claudia ^c   Ciccodicola, Alfredo ^a   Costa, Valerio ^a  

^a INSTITUTE OF GENETICS AND BIOPHYSICS ADRIANO BUZZATI TRAVERSO   (Italy)

^b UNIVERSITY OF SALERNO   (Italy)

^c CNR   (Italy)

^d SECOND UNIVERSITY OF NAPLES   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA; UNTRANSLATED RNA;

ARTICLE; CHROMOSOME 21; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; HUMAN; INFORMATION PROCESSING; INTERNET; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PILOT STUDY; REPRODUCIBILITY; SEQUENCE ANALYSIS;

BASE SEQUENCE; CHROMOSOMES, HUMAN, PAIR 21; COMPUTER SIMULATION; DATA COLLECTION; DATABASES, GENETIC; GENE EXPRESSION REGULATION; HUMANS; INTERNET; MICRORNAS; MOLECULAR SEQUENCE DATA; PILOT PROJECTS; REPRODUCIBILITY OF RESULTS; RNA, MESSENGER; RNA, UNTRANSLATED; SEQUENCE ANALYSIS, RNA;

EID: 84906546336     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bau009     Document Type: Article

References (46)

1. Kapranov, P., Cheng, J., Dike, S. et al. (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science, 316, 1484-1488.
2. Birney, E.J., Stamatoyannopoulos, A., Dutta, A. et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447, 799-816.
3. Jacquier, A. (2009) The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. Nat. Rev. Genet., 10, 833-844.
4. Clark, M.B., Amaral, P.P., Schlesinger, F.J. et al. (2011) The reality of pervasive transcription. PLoS Biol., 9, e1000625.
5. Harrow, J., Frankish, A., Gonzalez, J.M. et al. (2012) GENCODE: the reference human genome annotation for The ENCODE project. Genome Res., 9, 1760-1774.
6. Vervoort, R., Lennon, A., Bird, A.C. et al. (2000) Mutational hot spot within a new RPGR exon in X-linked retinitis pigmentosa. Nat. Genet., 25, 462-466.
7. Liu, G., Mattick, J.S. and Taft, R.J. (2013) A meta-analysis of the genomic and transcriptomic composition of complex life. Cell Cycle, 12, 2061-2072.
8. Barrett, L.W., Fletcher, S. and Wilton, S.D. (2012) Regulation of eukaryotic gene expression by the untranslated gene regions and other non-coding elements. Cell Mol. Life Sci., 69, 3613-3634.
9. Yandell, M. and Ence, D. (2012) A beginner's guide to eukaryotic genome annotation. Nat. Rev. Genet., 13, 329-342.
10. Costa, V., Angelini, C., De Feis, I. et al. (2010) Uncovering the complexity of transcriptomes with RNA-Seq. J. Biomed. Biotechnol., 2010, 853916.
11. Costa, V., Angelini, C., D'Apice, L. et al. (2011) Massive-scale RNA-Seq analysis of non ribosomal transcriptome in human trisomy 21. PLoS One, 6, e18493.
12. Trapnell, C., Pachter, L. and Salzberg, S.L. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.
13. Quinlan, A.R. and Hall, I.M. (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841-842.
14. Li, H., Handsaker, B., Wysoker, A. et al. (2009) The Sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079.
15. Zhang, Y., Liu, T., Meyer, C.A. et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol., 9, R137.
16. Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B, 57, 289-300.
17. van Helden, J. (2003) Regulatory sequence analysis tools. Nucleic Acids Res., 31, 3593-3596.
18. Huang, H.Y., Chien, C.H., Jen, K.H. et al. (2006) RegRNA: an integrated web server for identifying regulatory RNA motifs and elements. Nucleic Acids Res., 34, W429-W434.
19. Hofacker, I.L. (2003) Vienna RNA secondary structure server. Nucleic Acids Res., 31, 3429-3431.
20. Griffiths-Jones, S., Grocock, R.J., van Dongen, S. et al. (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res., 34, D140-D144.
21. Dweep, H., Sticht, C., Pandey, P. and Gretz, N. (2011) miRWalk-database: prediction of possible miRNA binding sites by "walking" the genes of three genomes. J. Biomed. Inform., 44, 839-847.
22. Gennarino, V.A., D'Angelo, G., Dharmalingam, G. et al. (2012) Identification of microRNA-regulated gene networks by expression analysis of target genes. Genome Res., 22, 1163-1172.
23. Oliveros, J.C. (2007) VENNY. An interactive tool for comparing lists with Venn Diagrams. http://bioinfogp.cnb.csic.es/tools/venny/index.html.
24. Tilgner, H., Raha, D., Habegger, L. et al. (2013) Accurate identification and analysis of human mRNA isoforms using deep long read sequencing. G3 (Bethesda), 3, 387-397.
25. Bartel, D.P. (2009) MicroRNAs: target recognition and regulatory functions. Cell, 136, 215-233.
26. Guo, H., Ingolia, N.T., Weissman, J.S. et al. (2010) Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature, 466, 835-840.
27. Salmena, L., Poliseno, L., Tay, Y. et al. (2011) A ceRNA hypothesis: the Rosetta stone of a hidden RNA language? Cell, 146, 353-368.
28. Cesana, M., Cacchiarelli, D., Legnini, I. et al. (2011) A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell, 147, 358-369.
29. Karreth, F.A., Tay, Y., Perna, D. et al. (2011) In vivo identification of tumor-suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma. Cell, 147, 382-395.
30. Tay, Y., Kats, L., Salmena, L. et al. (2011) Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell, 147, 344-357.
31. Costa, V., Esposito, R., Aprile, M. et al. (2012) Non-coding RNA and pseudogenes in neurodegenerative diseases: "The (un)Usual Suspects". Front. Genet., 3, 231.
32. Gruber, A.R., Lorenz, R., Bernhart, S.H. et al. (2008) The Vienna RNA websuite. Nucleic Acids Res., 36, W70-W74.
33. Pan, Q., Shai, O., Lee, L.J. et al. (2008) Deep surveying of alternative splicing complexity in the human transcriptome by highthroughput sequencing. Nat. Genet., 40, 1413-1415.
34. Keren, H., Lev-Maor, G. and Ast, G. (2010) Alternative splicing and evolution: diversification, exon definition and function. Nat. Rev. Genet., 11, 345-355.
35. Kornblihtt, A.R., Schor, I.E., Alló, M. et al. (2013) Alternative splicing: a pivotal step between eukaryotic transcription and translation. Nat. Rev. Mol. Cell Biol., 14, 153-165.
36. Binder, G., Brown, M. and Parks, J.S. (1996) Mechanisms responsible for dominant expression of human growth hormone gene mutations. J. Clin. Endocrinol. Metab., 81, 4047-4050.
37. Moseley, C.T., Mullis, P.E., Prince, M.A. et al. (2002) An exon splice enhancer mutation causes autosomal dominant GH deficiency. J. Clin. Endocrinol. Metab., 87, 847-852.
38. Faustino, N.A. and Cooper, T.A. (2003) Pre-mRNA splicing and human disease. Genes Dev., 17, 419-437.
39. Barbaux, S., Niaudet, P., Gubler, M.C. et al. (1997) Donor splice-site mutations in WT1 are responsible for Frasier syndrome. Nat. Genet., 17, 467-470.
40. Hossain, A. and Saunders, G.F. (2001) The human sex-determining gene SRY is a direct target of WT1. J. Biol. Chem., 276, 16817-16823.
41. Wilhelm, D. and Englert, C. (2002) The Wilms tumor suppressor WT1 regulates early gonad development by activation of Sf1. Genes Dev., 16, 1839-1851.
42. Bianchi, V., Colantoni, A., Calderone, A. et al. (2013) DBATE: database of alternative transcripts expression. Database (Oxford), 2013, bat050.
43. Bhartiya, D., Pal, K., Ghosh, S. et al. (2013) lncRNome: a comprehensive knowledgebase of human long noncoding RNAs. Database (Oxford), 2013, bat034.
44. Amaral, P.P., Clark, M.B., Gascoigne, D.K. et al. (2011) lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res., 39, D146-D151.
45. Bu, D., Yu, K., Sun, S. et al. (2012) NONCODE v3.0: integrative annotation of long noncoding RNAs. Nucleic Acids Res., 40, D210-D215.
46. Lam, H.Y., Khurana, E., Fang, G. et al. (2009) Pseudofam: the pseudogene families database. Nucleic Acids Res., 37, D738-D743.