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/mm9/mouse_TSS_v1.zip,
http://swissregulon.unibas.ch/data/mm9/mouse_TSC_v1.zip and
http://swissregulon.unibas.ch/data/mm9/mouse_TSR_v1.zip
Input file formats: GFF

Samples

From Mouse Jul. 2007 (NCBI37/mm9) Assembly

Filename Description Feature GEO-ID
1 mouse_TSS_v1.sga Transcription Start Sites TSS -
2 mouse_TSC_v1.sga Transcription Start Clusters TSC -
3 mouse_TSR_v1.sga Transcription Start 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