Genome-Wide Analysis of mRNA and Long Noncoding RNA Profiles in Chronic Actinic Dermatitis

Figure 2

Computational pipeline for the systematic filtration of CAD lncRNAs and mRNAs. (a) Bar chart of lncRNAs screening outcome in each step of the computational pipeline for the systematic identification of CAD lncRNAs and mRNAs. Step , transcripts with exons ≥ 2 were retained; Step , transcripts > 200 bp in length were retained; Step , transcripts with >3 reads coverage and 0.5 FPKM were retained; Step , known non-lncRNA annotations were identified as annotated lncRNAs, and known classes of RNAs, including known protein-coding genes, microRNAs, tRNAs, miscRNA, rRNAs, and pseudogenes, were eliminated; Step , transcripts without coding potential detected using CPC, CNCI, PFAM, and PhyloCSF were considered novel lncRNAs. (b) Coding potency filter with 4 mainstream coding potential analysis methods, including CPC analysis, CNCI analysis, FFAM, and PhyloCSF. (c) A Venn diagram describing the overlap between our catalog of CAD lncRNAs and those of Gencode v19. (d) Pie chart describing the classification of identified lncRNAs.

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