Genome annotation databases

At the heart of GenomeRunner lies genome annotation data from the ENCODE project. The human genome is big, and so are the (growing amount of) data generated by the ENCODE. Therefore, for the human genome I provide only a part of the genome annotation data, the best quality Tier 1 data hg19tier1.sqlite, and Tier2 data hg19tier2.sqlite. These files should be opened in GenomeRunner individually, to perform annotation/enrichment analyses against Tier 1 or Tier 2 data, respectively. Also, note the hg19tier100.sqlite file, containing cell type-specific transcription factor binding sites.

If more data are needed, such as Tier 3 data, or a combined dataset for all tiers, please, contact me directly on my gmail address, mikhail dot dozmorov.

Finally, genome annotation data for mouse are much less extensive. Therefore, mm9.sqlite contains all tiered mouse genome annotation data.