The HumMus Database

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The HumMus Database

• By Julie Graham, Ethan Wang, and Brian Pierce

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What is HumMus?

• Database contains alignments of mouse and human
  ortholog promoter regions.
• Also contains TRANSFAC hits for about 600
  transcription factors.
• The main idea the user can input a cluster of
  (coexpressed) genes to see what transcription
  factors are involved, and to what degree.

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Database Design and Data Sources

• ??? (Julie?)

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Program Design and Data Flow
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Interface

• Php program takes info from web forms and
  pre-processes it before passing it to processor

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Processor

• Written in perl for regular expression support,
  hash table support, database support
• Loads ortholog/gene alignments from database,
  determines transcription factors that co-occur in
  alignments
• Outputs position and number of transcription
  factor hits for gene, cluster and p-values

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(No Transcript)
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Interface Output Options
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Future Work

• Use different alignment schemes for the
  promoters.
• Incorporate data from more organisms.
• Less strict transcription factor matches between
  orthologs (can be plus or minus a few nucleotides)