SwissRegulon, database of genome-wide annotations of regulatory sites

Description

SwissRegulon annotation of Transcription Start Sites and Transcription Start Clusters generated with FANTOM4 CAGE data.

Source

Data available at:
http://swissregulon.unibas.ch/data/fantom4/promoters.gff.gz,
http://swissregulon.unibas.ch/data/hg19/hg19_TSC_v1.gff.gz and
http://swissregulon.unibas.ch/data/fantom4/tss_clusters_level3.gff.gz
Input file formats: GFF

Samples

From Human Feb. 2009 (GRCh37/hg19) Assembly. Available also for assembly GRCh36/hg18.

Filename Description Feature GEO-ID
1 promoters_hg19.sga Promoters TSS -
2 hg19_TSC_v1.sga Transcription Start Clusters TSC -
3 tss_clusters_level3_hg19.sga Promoters regions TSS -

Technical Notes

GFF files were converted in SGA. TSS were mapped to the 'Representative position' of the transcription start region. The files promoters_hg19.sga and tss_clusters_level3_hg19.sga are LiftedOver from hg18.

References

  1. Pachkov M, Balwierz PJ, Arnold P, Ozonov E, van Nimwegen E.
    SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates. Nucleic Acids Res. 2013, D214-20. PMID: 23180783