Zipper plot: visualizing transcriptional activity of genomic regions.
Francisco Avila CobosJasper AnckaertPieter-Jan VoldersCeline EveraertDries RombautJo VandesompeleKatleen De PreterPieter MestdaghPublished in: BMC bioinformatics (2017)
Using the Zipper plot, we found evidence of transcription for a set of well-characterized lncRNAs and observed that fewer mono-exonic lncRNAs have CAGE peaks overlapping with their TSSs compared to multi-exonic lncRNAs. Using publicly available RNA-seq data, we found more than one hundred cases where junction reads connected protein-coding gene exons with a downstream mono-exonic lncRNA, revealing the need for a careful evaluation of lncRNA 5'-boundaries. Our method is implemented using the statistical programming language R and is freely available as a webtool.
Keyphrases
- rna seq
- genome wide identification
- transcription factor
- single cell
- genome wide analysis
- network analysis
- copy number
- long non coding rna
- long noncoding rna
- gene expression
- autism spectrum disorder
- genome wide
- protein protein
- amino acid
- living cells
- binding protein
- machine learning
- deep learning
- heat shock protein
- fluorescent probe