Yeast gene regulation database

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Yeast gene regulation database
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• Dr Jaak Vilo group
• Department of Bioinformatics
• University of Tartu, Estonia

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Currently

• We are creating a database for integrating
  various data sources for the purpose of studying
  gene regulation.
• We are working with signals and motifs in DNA.

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DNA motifs and signals

• known transcription factor binding sites
• in silico prediction of de novo predicted
  putative binding sites
• in vitro obtained binding sites

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We model

• various representations of binding sites, both
  deterministic and probabilistic
• the gene regulatory networks

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• Data integration from various data sources
• cross-linking to used sources and to other data
  sources, which are not integrated

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So far

• We have worked out database schema

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So far

• We have integrated data from various sources
• Current databases SCPD
• Articles Kellis et al, Nature 2003
• Our own putative sites Vilo et al

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Binding sites representations

• Strings
• Consensus sequences
• Regular expressions
• Matrices

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Next steps

• Web interface
• Gene regulation modelling
• Quality assesment based on source data
• Tools and integration with EP (Expression
  Profiler)