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refTSS: A Reference Data Set for Human and Mouse Transcription Start Sites
Imad Abugessaisa1, Shuhei Noguchi1, Akira Hasegawa1
1RIKEN Center for Integrative Medical Sciences, 1-7-22, Suehiro-Cho, Tsurumi-Ku, Yokohama, Kanagawa 230-0045, Japan.
Journal of Molecular Biology
|May 11, 2019
Summary
Researchers created refTSS, a comprehensive human and mouse genome dataset of transcription start sites (TSSs), integrating multiple resources. This provides a unified view for studying RNA production and transcriptional regulation.
Area of Science:
- Genomics
- Transcriptomics
- Bioinformatics
Background:
- Transcription start sites (TSSs) are key regulatory points for RNA production.
- Existing TSS datasets are fragmented, hindering comprehensive analysis.
- Integrating diverse data sources around TSSs is crucial for understanding transcriptional regulation.
Purpose of the Study:
- To construct a comprehensive reference dataset of human and mouse transcription start sites (TSSs).
- To integrate publicly available TSS annotations and promoter resources into a unified dataset.
- To provide a browsable web interface for accessing and utilizing the refTSS resource.
Main Methods:
- Collected and integrated TSS annotations from FANTOM5, DBTSS, EPDnew, and ENCODE.
- Compiled genomic coordinates, gene annotations, quality checks, and conservation data for TSSs.
- Developed a web interface for interactive exploration of the refTSS dataset.
Main Results:
- Established refTSS, a comprehensive reference dataset for human and mouse TSSs.
- The dataset includes genomic coordinates, gene annotations, quality metrics, and cross-species conservation.
- A user-friendly web portal (http://reftss.clst.riken.jp/) is available for data access.
Conclusions:
- refTSS serves as a valuable, integrated resource for studying transcriptional regulation and RNA production.
- The dataset facilitates data collection and integration for researchers in genomics and transcriptomics.
- The web interface enhances accessibility and usability of TSS information for the scientific community.
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