Figure 1 | Scientific Reports

Figure 1

From: CCIVR facilitates comprehensive identification of cis-natural antisense transcripts with their structural characteristics and expression profiles

Figure 1

Overview of CCIVR and the processing steps of its pipeline. (A) Definition of four types of cis-NAT analyzed in this study, “embedded”, “fully-overlapped”, “head-to-head”, and “tail-to-tail”, which can be identified by CCIVR. TSS: transcription start site; TTS: transcription termination site. (B) Overview of CCIVR. The program generates a list of all cis-NAT types from a processed RNA-seq data. The processed RNA-seq data must contain five different gene annotation columns including “id”, “Chr”, “Strand”, “Start”, and “End”. Attaching information for expression profiling obtained from RNA-seq analysis is also available such as “TPM”, “FPKM”, “fold-change”, and “padj”. For details, please see README.md file placed at https://github.com/CCIVR/ccivr. (C) An example of the process for a target gene, Xist, and identification of its cis-NAT, Tsix, during the process that identifies fully-overlapped cis-NATs from minus to plus strand.

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