Differential expression

RPKM value was used for expression analysis. We used DEGseq for differential expression analysis of these results. S. scofa lncRNAs and protein-coding genes showing a fold change ≥2 and q < 0.05 were considered to be differentially expressed.

Brwose by classfication

Terms of intergenic, intronic and cis-regulatory region was used to demonstrate lncRNA located at intergenic region, intronic region and cis-regulatory region on genome. Terms like antisense- was illustrated genomic organization of lncRNA overlapped antisense transcripts of “protein_coding”, miRNA and “processed_transcript”.

Sequences conservation

We used pairwise alignments produced by the UCSC comparative genomics pipeline (N1,N2). We analyzed the files in overlapping chain format and defined a conserved lncRNA when 50% of its nucleotides uniquely intersected with an alignment in the chain file.

PHM means lncRNA was conserved among human, mouse and pig.

HU means lncRNA was conservation when comparing with human.

MO means lncRNA was conservation when comparing with mouse.

"no" means lncRNA was not conservation among human, mouse and pig.

Weng et al

Genomics. 2017 Oct;109(5-6):446-456. doi: 10.1016/j.ygeno.2017.07.001.
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Shen Y, Mao H, Huang M, Chen L, Chen J, Cai Z, Wang Y, Xu N.

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Biomed Res Int. 2017;2017:6152582. doi: 10.1155/2017/6152582.
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Pipeline

See document

Note

N1, Washietl, S., Kellis, M. and Garber, M. 2014, Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals. Genome Res, 24, 616-628.

N2, Rosenbloom, K. R., Armstrong, J., Barber, G. P., et al. 2015, The UCSC Genome Browser database: 2015 update. Nucleic Acids Res, 43, D670-681.

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