Tiffin

Tiffin is a database of predicted regulatory motifs and predicted functional sites ("motif instances") on genome sequences. Over-represented motifs are discovered from large stretches of genomic sequence using the NestedMICA algorithm, then validated on the basis of correlations with sequence conservation and gene expression patterns. Having obtained this motif set, it is used to scan likely regulatory regions of the genome to give a set of predicted motif instances. Tiffin is developed in the Tim Hubbard's Vertebrate Genome Analysis research group at the Wellcome Trust Sanger Institute.

[Genome Research Limited]

Motif collections

Tiffin version 1.2 was released in October 2006 and consists of 120 putative transcription factor binding motifs from the fruitfly Drosophila melanogaster.

The Tiffin 1.2 motif set is described in the following publication:

  • Large-scale discovery of promoter motifs in Drosophila melanogaster.

    Down TA, Bergman CM, Su J and Hubbard TJ

    PLoS computational biology 2007;3;1;e7

    PUBMED: 17238282; PMC: 1779301; DOI: 10.1371/journal.pcbi.0030007

Genome annotation

You can also view predicted binding sites on the fruitfly genome via Ensembl (example). Note that this is currently based on the Tiffin 1.0 motif set, and includes a slightly different mapping of motif to developmental terms (based on looking at motif matches in predicted enhancer regions, rather than promoters.

  • View Tiffin 1.0 motifs: future releases will include a more comprehensive set of fly motifs, and motif predictions for other Ensembl species.
  • View Tiffin 1.1 motifs: note that, from Tiffin 1.1 onwards, motif identifiers have been generalised to include a 3 letter species name, following the convention used in Ensembl, in preparation for supporting motif sets from other species.
* quick link - http://q.sanger.ac.uk/1adys2g9