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Zipper plot : visualizing transcriptional activity of genomic regions

Francisco Avila Cobos (UGent) , Jasper Anckaert (UGent) , Pieter-Jan Volders (UGent) , Celine Everaert (UGent) , Dries Rombaut (UGent) , Jo Vandesompele (UGent) , Katleen De Preter (UGent) and Pieter Mestdagh (UGent)
Author
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Abstract
Reconstructing transcript models from RNA-sequencing (RNA-seq) data and establishing these as independent transcriptional units can be a challenging task. Current state-of-the-art tools for long non-coding RNA (lncRNA) annotation are mainly based on evolutionary constraints, which may result in false negatives due to the overall limited conservation of lncRNAs. To tackle this problem we have developed the Zipper plot, a novel visualization and analysis method that enables users to simultaneously interrogate thousands of human putative transcription start sites (TSSs) in relation to various features that are indicative for transcriptional activity. These include publicly available CAGE-sequencing, ChIPsequencing and DNase-sequencing datasets. Our method only requires three tab-separated fields (chromosome, genomic coordinate of the TSS and strand) as input and generates a report that includes a detailed summary table, a Zipper plot and several statistics derived from this plot. 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. Our method is implemented using the statistical programming language R and is freely available as a webtool.
Keywords
Transcriptomics, long non-coding RNAs, bioinformatics

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Chicago
Avila Cobos, Francisco, Jasper Anckaert, Pieter-Jan Volders, Celine Everaert, Dries Rombaut, Jo Vandesompele, Katleen De Preter, and Pieter Mestdagh. 2018. “Zipper Plot : Visualizing Transcriptional Activity of Genomic Regions.” In Belgian Society for Human Genetics, 18th Annual Meeting, Abstracts.
APA
Avila Cobos, F., Anckaert, J., Volders, P.-J., Everaert, C., Rombaut, D., Vandesompele, J., De Preter, K., et al. (2018). Zipper plot : visualizing transcriptional activity of genomic regions. Belgian Society for Human Genetics, 18th Annual meeting, Abstracts. Presented at the 18th Annual BeSHG meeting: The epigenome in development and disease.
Vancouver
1.
Avila Cobos F, Anckaert J, Volders P-J, Everaert C, Rombaut D, Vandesompele J, et al. Zipper plot : visualizing transcriptional activity of genomic regions. Belgian Society for Human Genetics, 18th Annual meeting, Abstracts. 2018.
MLA
Avila Cobos, Francisco, Jasper Anckaert, Pieter-Jan Volders, et al. “Zipper Plot : Visualizing Transcriptional Activity of Genomic Regions.” Belgian Society for Human Genetics, 18th Annual Meeting, Abstracts. 2018. Print.
@inproceedings{8564261,
  abstract     = {Reconstructing transcript models from RNA-sequencing (RNA-seq) data and establishing these as independent transcriptional units can be a challenging task. Current state-of-the-art tools for long non-coding RNA (lncRNA) annotation are mainly based on evolutionary constraints, which may result in false negatives due to the
overall limited conservation of lncRNAs.
To tackle this problem we have developed the Zipper plot, a novel visualization and analysis method that enables users to simultaneously interrogate thousands of human putative transcription start sites (TSSs) in relation to various features that are indicative for transcriptional activity. These include publicly available CAGE-sequencing, ChIPsequencing
and DNase-sequencing datasets. Our method only requires three tab-separated fields (chromosome, genomic coordinate of the TSS and strand) as input and generates a report that includes a detailed summary table, a Zipper plot and several statistics derived from this plot.
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. Our method is implemented using the statistical programming language R and is freely available as a webtool.},
  author       = {Avila Cobos, Francisco and Anckaert, Jasper and Volders, Pieter-Jan and Everaert, Celine and Rombaut, Dries and Vandesompele, Jo and De Preter, Katleen and Mestdagh, Pieter},
  booktitle    = {Belgian Society for Human Genetics, 18th Annual meeting, Abstracts},
  keyword      = {Transcriptomics,long non-coding RNAs,bioinformatics},
  language     = {eng},
  location     = {Ghent, Belgium},
  title        = {Zipper plot : visualizing transcriptional activity of genomic regions},
  year         = {2018},
}