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Meeting Notes for July 1, 2003

Dr. Grene, Johnathan, and Ceci are back from Europe, and Ranjit is going on vacation for the summer.

Last week John A. finished two scripts.

1. One creates a database table for gene ontology categories, so relevant data may be included in reports.
2. Another draws images illustrating locations of known regulatory sequences.

The images of regulatory sequences sometimes contain too much data to be reasonably interpreted by a human. Possible solutions for this are

• The patterns for elements might be too generic; finding more specific patterns, if possible, could create fewer results.
• Limit the results to hits within the first 1,000 bp of the upstream region.
• Find characteristics of a match and assign a score to each element based on those characteristics. Then only show characteristics with a score above some arbitrary value. Possible characteristics for determining a score are
  • If an element has known flanking sequences, a higher score should be assigned.
  • If many promoters of a certain type are found many times in one area, they are probably part of some repeat and should be given a lower score.
  • We can use a program to analyze upstream regions for sequence redundancy. If a region contains similar sequences repeated many times, we will assign a lower score to elements found in that region.

When many elements are found for a gene, this is usually because the upstream region is huge. Only displaying elements within 1 kb of the coding region should filter out most of the results. One possible cause for huge upstream regions is that the gene is near a centromere.

Human TonE elements (a dehydration response element) are found nearly twice to three times as often as probability indicates on chromosome. This is not terribly surprising because TonE elements perform a biological function. In the future John A. will count the number of TonE elements occurring within a coding region and the TonE element that occur between coding regions.