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Meeting Notes for June 3, 2003

Attendance: Ruth Grene, Lenny Heath, John Hanks, Ranjit Randhawa, John Archie, Naren Ramakrishnan, Steve Slaughter, Xiaofeng Bao.

The promoter website has the three papers Dr Ramakrishnan suggested.

1. Fickett JW, Hatzigeorgiou AG.
   
   Eukaryotic Promoter Recognition.
   
   Genome Research.1997;7:861-878.
2. Zhang MQ.
   
   Identification of Human Gene Core Promoters in Silico
   
   Genome Research.1998;8:319-328.
3. Pedersen AG, Baldi P, Chauvin Y, Brunak S.
   
   The biology of eukaryotic promoter prediction - a review
   
   Computers and Chemistry.1999:23:191-207.

They can all be found at the selected papers page of the promoters website

There are a number of promoter databases of which EPD and PlantProm are two examples.

For database purposes the definition of a promoter is a DNA sequence around a transcription initiation site.

EPD is the Eukaryotic Promoter Database. It is a non-redundant collection of eukaryotic POL II promoters. There are different types of entries in the database, these include:

• TATA
• TATA-less, Inr
• Both TATA and Inr
• neither TATA or Inr
• TATA-less, Inr, DPE

Dr Ramakrishnan provided a detailed description of the structure of an EPD entry (To know how to parse and use links). Important fields are the FP line. Breakdown of FP line is as follows:

1-2|3-5----|6-30----------------|31-55-----------------------| //(CHARACTER NUMBERS)
FP  [blank]            ...P2+:+S EM:X00364              1+      2490; 11148.053 010*2
                           |   |  |   |                 |        |         |
                           |   |  |   |                 |        |         |
                   promoter 2  |  |  EMBL accession #   |        |  Alternative id numbers
                               |  |                     |        |
        promoter of type "Single" |                     |     Position in sequence
       (Single initiation site)   |                     |
                                 EMBL database       Linear sequence
                                                     (plus sign denotes which strand)

We will look at response elements (RE).

• Modularity of RE
• Proteins who bind upstream and become associated with complex
• create templates
• understand S/M entries in EPD database
• understand how RE participates with machinery

How are REs triggered and how can Transcription Factor databases help us?

Things todo:

• Want to look upstream
• Want to clump them in modularity
• Want to classify genes with a particular type of modularity
• Assume databases are complete in their coverage of Initiation Sites (IS)
• Look at REs we are interested in.
• We want to figure out how to interpret Initiation Start Sites (ISS)

A note about using multiple databases:

There could be entries in common in both databases. Use common sequences for HSE,ARE,etc (list Dr Grene gave Ranjit)