References
- Quan M , ChenJ , ZhangD . Exploring the secrets of long noncoding RNAs . Int. J. Mol. Sci.16 ( 3 ), 5467 – 5496 ( 2015 ).
- Wang L , TangH , XiongY , TangL . Differential expression profile of long noncoding RNAs in human chorionic villi of early recurrent miscarriage . Clin. Chim. Acta464 , 17 – 23 ( 2017 ).
- Necsulea A , SoumillonM , WarneforsMet al. The evolution of lncRNA repertoires and expression patterns in tetrapods . Nature505 ( 7485 ), 635 – 640 ( 2014 ).
- Wei S , WangK . Long noncoding RNAs: pivotal regulators in acute myeloid leukemia . Exp. Hematol. Oncol.5 ( 1 ), 30 ( 2016 ).
- Wapinski O , ChangHY . Long noncoding RNAs and human disease . Trends Cell Biol.21 ( 6 ), 354 – 361 ( 2011 ).
- Faghihi MA , ModarresiF , KhalilAMet al. Expression of a noncoding RNA is elevated in Alzheimer’s disease and drives rapid feed-forward regulation of β-secretase expression . Nat. Med.14 ( 7 ), 723 ( 2008 ).
- Bassols A , CostaC , EckersallPD , OsadaJ , SabriaJ , TibauJ . The pig as an animal model for human pathologies: a proteomics perspective . Proteomics Clin. Appl.8 ( 9–10 ), 715 – 731 ( 2014 ).
- Yu L , TaiL , ZhangL , ChuY , LiY , ZhouL . Comparative analyses of long non-coding RNA in lean and obese pig . Oncotarget8 ( 25 ), 41440 – 41450 ( 2017 ).
- Li J , GaoZ , WangX , LiuH , ZhangY , LiuZ . Identification and functional analysis of long intergenic noncoding RNA genes in porcine pre-implantation embryonic development . Sci. Rep.6 , 38333 ( 2016 ).
- Wang Y , HuT , WuL , LiuX , XueS , LeiM . Identification of noncoding and coding RNAs in porcine endometrium . Genomics109 ( 1 ), 43 – 50 ( 2017 ).
- Zhou Z-Y , LiA-M , AdeolaACet al. Genome-wide identification of long intergenic noncoding RNA genes and their potential association with domestication in pigs . Genome Biol. Evol.6 ( 6 ), 1387 – 1392 ( 2014 ).
- Index of ftp://ftp.ensembl.org/pub/release-67/fasta/sus_scrofa/dna/ . ftp://ftp.ensembl.org/pub/release-67/fasta/sus_scrofa/dna/ .
- Index of /pub/release-82/gff3/sus_scrofa/ . http://ftp.ensembl.org/pub/release-82/gff3/sus_scrofa/ .
- ALDB: a domestic-animal long noncoding RNA database . http://res.xaut.edu.cn/aldb/index.jsp .
- Splicing express . https://bitbucket.org/jekroll/splicingexpress/ .
- MCScanX: Multiple Collinearity Scan toolkit . http://chibba.pgml.uga.edu/mcscan2/ .
- Pertea M , PerteaGM , AntonescuCM , ChangTC , MendellJT , SalzbergSL . StringTie enables improved reconstruction of a transcriptome from RNA-seq reads . Nat. Biotechnol.33 ( 3 ), 290 – 295 ( 2015 ).
- Sun L , LuoH , BuDet al. Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts . Nucleic Acids Res.41 ( 17 ), e166 ( 2013 ).
- Li A , ZhangJ , ZhouZ , WangL , LiuY , LiuY . ALDB: a domestic-animal long noncoding RNA database . PLoS ONE10 ( 4 ), e0124003 ( 2015 ).
- Ma L , BajicVB , ZhangZ . On the classification of long non-coding RNAs . RNA Biol.10 ( 6 ), 925 – 933 ( 2013 ).
- Derrien T , JohnsonR , BussottiGet al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression . Genome Res.22 ( 9 ), 1775 – 1789 ( 2012 ).
- Kornienko AE , DotterCP , GuenzlPMet al. Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans . Genome Biol.17 , 14 ( 2016 ).
- Kellis M , WoldB , SnyderMPet al. Defining functional DNA elements in the human genome . Proc. Natl Acad. Sci. USA111 ( 17 ), 6131 – 6138 ( 2014 ).
- Xiao S , XieD , CaoXet al. Comparative epigenomic annotation of regulatory DNA . Cell149 ( 6 ), 1381 – 1392 ( 2012 ).
- Peschansky VJ , WahlestedtC . Non-coding RNAs as direct and indirect modulators of epigenetic regulation . Epigenetics9 ( 1 ), 3 – 12 ( 2014 ).
- Jiang C , LiY , ZhaoZet al. Identifying and functionally characterizing tissue-specific and ubiquitously expressed human lncRNAs . Oncotarget7 ( 6 ), 7120 – 7133 ( 2016 ).
- Louro R , SmirnovaAS , Verjovski-AlmeidaS . Long intronic noncoding RNA transcription: expression noise or expression choice?Genomics93 ( 4 ), 291 – 298 ( 2009 ).
- Szczesniak MW , MakalowskaI . lncRNA-RNA interactions across the human transcriptome . PLoS ONE11 ( 3 ), e0150353 ( 2016 ).
- Bardou F , ArielF , SimpsonCGet al. Long noncoding RNA modulates alternative splicing regulators in Arabidopsis . Dev. Cell30 ( 2 ), 166 – 176 ( 2014 ).
- Hezroni H , KoppsteinD , SchwartzMG , AvrutinA , BartelDP , UlitskyI . Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species . Cell Rep.11 ( 7 ), 1110 – 1122 ( 2015 ).
- Lindskog C . The potential clinical impact of the tissue-based map of the human proteome . Expert. Rev. Proteomics12 ( 3 ), 213 – 215 ( 2015 ).
- Zhao Y , LiuW , ZengJet al. Identification and analysis of mouse non-coding RNA using transcriptome data . Sci. China Life Sci.59 ( 6 ), 589 – 603 ( 2016 ).