ALDB:A domestic-animal long noncoding RNA database

PLoS ONE

Volumn 10, Issue 4, 2015, Pages

  Li, Aimin ^a,b   Zhang, Junying ^a   Zhou, Zhongyin ^c,d   Wang, Lei ^b   Liu, Yujuan ^e   Liu, Yajun ^a,b  

^a XIDIAN UNIVERSITY   (China)

^b XI'AN UNIVERSITY OF TECHNOLOGY   (China)

^c UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^d KUNMING INSTITUTE OF ZOOLOGY   (China)

^e CCCC First Highway   (China)

Author keywords

[No Author keywords available]

Indexed keywords

LONG UNTRANSLATED RNA;

ARTICLE; BIOINFORMATICS; CHICKEN; COMPUTER INTERFACE; CONTROLLED STUDY; COW; DOMESTIC ANIMAL; DOMESTICATION; GENE EXPRESSION PROFILING; GENETIC DATABASE; GENETIC VARIABILITY; INFORMATION STORAGE; NONHUMAN; ONLINE SYSTEM; QUANTITATIVE TRAIT LOCUS; RNA SEQUENCE; ANIMAL; BOVINE; CLASSIFICATION; FEMALE; GENETICS; MOLECULAR GENETICS; NUCLEIC ACID DATABASE; PIG; SOFTWARE;

ANIMALIA; SUIDAE;

ANIMALS; ANIMALS, DOMESTIC; CATTLE; CHICKENS; DATABASES, NUCLEIC ACID; FEMALE; MOLECULAR SEQUENCE ANNOTATION; QUANTITATIVE TRAIT LOCI; RNA, LONG NONCODING; SOFTWARE; SWINE;

EID: 84928914391     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0124003     Document Type: Article

References (48)

1. Ulitsky I, Bartel DP. lincRNAs: genomics, evolution, and mechanisms. Cell 2013; 154: 26-46. doi: 10. 1016/j.cell.2013.06.020 PMID: 23827673
2. Li L, Eichten SR, Shimizu R, Petsch K, Yeh C-T, Wu W, et al. Genome-wide discovery and characterization of maize long non-coding RNAs. Genome Biol 2014; 15: R40. doi: 10.1186/gb-2014-15-2-r40 PMID: 24576388
3. Wang H, Chung PJ, Liu J, Jang I-C, Kean M, Xu J, et al. Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis. Genome Res 2014: gr. 165555.165113.
4. Duret L. , ChureauC., SamainS., WeissenbachJ., AvnerP. The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene. Science 2006; 312: 1653-1655. PMID: 16778056 5.
5. ∅ rom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, et al. Long noncoding RNAs with enhancer-like function in human cells. Cell 2010; 143: 46-58. doi: 10.1016/j.cell.2010.09.001 PMID: 20887892
6. Lee JT. Epigenetic regulation by long noncoding RNAs. Science 2012; 338: 1435-1439. doi: 10.1126/ science.1231776 PMID: 23239728
7. Esteve-Codina A, Kofler R, Palmieri N, Bussotti G, Notredame C, Pérez-Enciso M. Exploring the gonad transcriptome of two extreme male pigs with RNA-seq. BMC Genomics 2011; 12: 552. doi: 10.1186/ 1471-2164-12-552 PMID: 22067327
8. Li T, Wang S, Wu R, Zhou X, Zhu D, Zhang Y. Identification of long non-protein coding RNAs in chicken skeletal muscle using next generation sequencing. Genomics 2012; 99: 292-298. doi: 10.1016/j. ygeno.2012.02.003 PMID: 22374175
9. Weikard R, Hadlich F, Kuehn C. Identification of novel transcripts and noncoding RNAs in bovine skin by deep next generation sequencing. BMC Genomics 2013; 14: 789. doi: 10.1186/1471-2164-14-789 PMID: 24225384
10. Qu Z, Adelson DL. Bovine ncRNAs are abundant, primarily intergenic, conserved and associated with regulatory genes. PLoS One 2012; 7: e42638. doi: 10.1371/journal.pone.0042638 PMID: 22880061
11. Huang W, Long N, Khatib H. Genome-wide identification and initial characterization of bovine long non-coding RNAs from EST data. Anim Genet 2012; 43: 674-682. doi: 10.1111/j.1365-2052.2012. 02325.x PMID: 22497321
12. Zhou ZY, Li AM, Adeola AC, Liu YH, Irwin DM, Xie HB, et al. Genome-wide identification of long intergenic noncoding RNA genes and their potential association with domestication in pigs. Genome Biol Evol 2014; 6: 1387-1392. doi: 10.1093/gbe/evu113 PMID: 24891613
13. Xie C, Yuan J, Li H, Li M, Zhao G, Bu D, et al. NONCODEv4: exploring the world of long non-coding RNA genes. Nucleic Acids Res 2014; 42: D98-D103. doi: 10.1093/nar/gkt1222 PMID: 24285305
14. Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS. lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res 2011; 39: D146-151. doi: 10.1093/nar/gkq1138 PMID: 21112873
15. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 2011; 25: 1915-1927. doi: 10.1101/gad.17446611 PMID: 21890647
16. Kutter C. , WattS., StefflovaK., WilsonM.D., GoncalvesA., PontingC.P., et al. Rapid turnover of long noncoding RNAs and the evolution of gene expression. PLoS Genet 2012; 8: e1002841. doi: 10.1371/ journal.pgen.1002841 PMID: 22844254 17.
17. Ø rom UA, Shiekhattar R. Long noncoding RNAs usher in a new era in the biology of enhancers. Cell 2013; 154: 1190-1193. doi: 10.1016/j.cell.2013.08.028 PMID: 24034243
18. Jin J, Liu J, Wang H, Wong L, Chua NH. PLncDB: plant long non-coding RNA database. Bioinformatics 2013; 29: 1068-1071. doi: 10.1093/bioinformatics/btt107 PMID: 23476021
19. Dinger ME, Pang KC, Mercer TR, Crowe ML, Grimmond SM, Mattick JS. NRED: a database of long noncoding RNA expression. Nucleic Acids Res 2009; 37: D122-126. doi: 10.1093/nar/gkn617 PMID: 18829717
20. Chen G, Wang Z, Wang D, Qiu C, Liu M, Chen X, et al. LncRNADisease: a database for long-non-coding RNA-associated diseases. Nucleic Acids Res 2013; 41: D983-986. doi: 10.1093/nar/gks1099 PMID: 23175614
21. Volders PJ, Helsens K, Wang X, Menten B, Martens L, Gevaert K, et al. LNCipedia: a database for annotated human lncRNA transcript sequences and structures. Nucleic Acids Res 2013; 41: D246-251. doi: 10.1093/nar/gks915 PMID: 23042674
22. Niazi F, Valadkhan S. Computational analysis of functional long noncoding RNAs reveals lack of pep-tide-coding capacity and parallels with 30 UTRs. RNA 2012; 18: 825-843. doi: 10.1261/rna.029520.111 PMID: 22361292
23. Yang J-H, Li J-H, Jiang S, Zhou H, Qu L-H. ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. Nucleic Acids Res 2012.
24. Li J-H, Liu S, Zhou H, Qu L-H, Yang J-H. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res 2014; 42: D92-D97. doi: 10.1093/nar/gkt1248 PMID: 24297251
25. Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, et al. Ensembl 2014. Nucleic Acids Res 2014; 42: D749-D755. doi: 10.1093/nar/gkt1196 PMID: 24316576
26. Jia H, Osak M, Bogu GK, Stanton LW, Johnson R, Lipovich L. Genome-wide computational identification and manual annotation of human long noncoding RNA genes. RNA 2010; 16: 1478-1487. doi: 10. 1261/rna.1951310 PMID: 20587619
27. Liu J, Jung C, Xu J, Wang H, Deng S, Bernad L, et al. Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell 2012; 24: 4333-4345. doi: 10.1105/tpc.112. 102855 PMID: 23136377
28. Albert FW, Somel M, Carneiro M, Aximu-Petri A, Halbwax M, Thalmann O, et al. A comparison of brain gene expression levels in domesticated and wild animals. PLoS Genet 2012; 8: e1002962. doi: 10. 1371/journal.pgen.1002962 PMID: 23028369
29. Brawand D, Soumillon M, Necsulea A, Julien P, Csárdi G, Harrigan P, et al. The evolution of gene expression levels in mammalian organs. Nature 2011; 478: 343-348. doi: 10.1038/nature10532 PMID: 22012392
30. Merkin J, Russell C, Chen P, Burge CB. Evolutionary dynamics of gene and isoform regulation in Mammalian tissues. Science 2012; 338: 1593-1599. doi: 10.1126/science.1228186 PMID: 23258891
31. Barbosa-Morais NL, Irimia M, Pan Q, Xiong HY, Gueroussov S, Lee LJ, et al. The evolutionary landscape of alternative splicing in vertebrate species. Science 2012; 338: 1587-1593. doi: 10.1126/ science.1230612 PMID: 23258890
32. Acland A, Agarwala R, Barrett T, Beck J, Benson DA, Bollin C, et al. Database resources of the national center for biotechnology information. Nucleic Acids Res 2013; 41: D8-D20. doi: 10.1093/nar/gks1189 PMID: 23193264
33. Ponting CP, Oliver PL, Reik W. Evolution and functions of long noncoding RNAs. Cell 2009; 136: 629-641. doi: 10.1016/j.cell.2009.02.006 PMID: 19239885
34. Kong L, Zhang Y, Ye ZQ, Liu XQ, Zhao SQ, Wei L, et al. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res 2007; 35: W345-349. PMID: 17631615
35. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 2012; 7: 562-578. doi: 10.1038/nprot.2012.016 PMID: 22383036
36. Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res 2002; 12: 656-664. PMID: 11932250
37. Aboyoun P, Pages H, Lawrence M (2013) GenomicRanges: Representation and manipulation of genomic intervals.
38. Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol 2010; 11: R106. doi: 10.1186/gb-2010-11-10-r106 PMID: 20979621
39. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010; 26: 139-140. doi: 10.1093/ bioinformatics/btp616 PMID: 19910308
40. Consortium CT. The nature and identification of quantitative trait loci: a community's view. Nat Rev Genet 2003; 4: 911. PMID: 14634638
41. Hu ZL, Park CA, Wu XL, Reecy JM. Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era. Nucleic Acids Res 2013; 41: D871-879. doi: 10.1093/nar/gks1150 PMID: 23180796
42. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, et al. The generic genome browser: a building block for a model organism system database. Genome Res 2002; 12: 1599-1610. PMID: 12368253
43. Altschul SF,Madden TL, Schäffer AA, Zhang J, Zhang Z,MillerW, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25: 3389-3402. PMID: 9254694
44. Warren ST, Schalling DEHcM. Tissue specific expression of FMR-1 provides evidence for a functional role in fragile X syndrome. Nat Genet 1993; 3.
45. Sun L, Luo H, Bu D, Zhao G, Yu K, Zhang C, et al. Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Res 2013; 41: e166. doi: 10.1093/nar/ gkt646 PMID: 23892401
46. Prensner JR, Iyer MK, Balbin OA, Dhanasekaran SM, Cao Q, Brenner JC, et al. Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol 2011; 29: 742-749. doi: 10.1038/nbt.1914 PMID: 21804560
47. Andersson L, Georges M. Domestic-animal genomics: deciphering the genetics of complex traits. Nature Reviews Genetics 2004; 5: 202-212. PMID: 14970822
48. Roberts R, Smith G, Bazer F, Cibelli J, Seidel G, Bauman D, et al. Farm animal research in crisis. Science 2009; 324: 468. doi: 10.1126/science.1168521 PMID: 19390030