• If proteins A, B, C & D are increased, and proteins H & K are decreased, what disease entities might be present?
• For a given disease, specifically what pattern of fold changes might be expected for proteins A, D & H?
• As a practical example: the patient has a lesion in the lung, but is it an infection or a tumor? What differences are seen in the APP patterns in each case - i.e. which sets of protein changes are important?

Diseases

1. What diseases have fold changes with protein K? - changes of > 5X?
2. What diseases have fold increases > 2.0X for protein A & B, and decreases < 2.5X for protein C & D?
3. Which diseases have a 0.5X fold change (i.e decrease) in this protein? - in `all' the proteins in the database?
4. Compare protein patterns that change for diseases A & B.

Proteins}

1. What proteins have fold changes associated with this disease? How much do they change? How much do they change in plasma? in urine?
2. Which proteins change by more than 1.5X fold change (i.e. increase) in this disease?
3. Where are these proteins in the serum (urine, CSF, etc) reference 2-DE gel map? any 2-DE gel map?
4. What is the name of this protein I am pointing to in the plasma 2-DE gel map? What diseases is it involved in?
5. Show a 2-DE gel map of plasma proteins that increase in this disease in red and those that decrease in blue.

Literature references

1. What literature references discuss these proteins in the context of these diseases?
2. What literature references for disease Q had more than N patients in the study?
3. Who has worked on this protein?

1. It reports a controlled randomized clinical study.
2. It discusses a protein disease relationship in a clinical study describing quantitative protein changes (by some protein assay method) and the diseases or conditions involved.
3. The data are from a refereed journal article (books and certified databases etc. are being considered for use, but are not used now).
4. It includes concentration fold changes and values for disease and normal states.
5. It includes the number of patients in both the normal (control) and disease (case) populations used in a study.
6. A p-value for the difference in protein concentration between groups is given or can be calculated.

a) Initial SQL query statement

  SELECT protein.prot_id, protein.prot_name, 
         dis_correl.fold_change, condition.cond_name
    FROM protein, dis_correl, condition, source
    WHERE
  {+ use_source_name
     (dis_correl.source_id = source.source_id) AND
     (source.source_name = '$source_name$') AND
  }+
     ((
  {+ use_fold_change
      (dis_correl.fold_change .GT. $fold_change_lower_bnd$) AND
      (dis_correl.fold_change .LT. $fold_change_upper_bnd$) AND
  }+
      (condition.cond_name = '$cond_name$') AND
      (condition.cond_id = dis_correl.cond_id) AND
      (dis_correl.prot_id = protein.prot_id))
       )


b) Expanded SQL query statement

  SELECT protein.prot_id, protein.prot_name, 
         dis_correl.fold_change, condition.cond_name
    FROM protein, dis_correl, condition, source
    WHERE
     ((
      (dis_correl.fold_change >  2.0) AND
      (dis_correl.fold_change <  5.0) AND
      (condition.cond_name = 'Bladder Carcinoma N0') AND
      (condition.cond_id = dis_correl.cond_id) AND
      (dis_correl.prot_id = protein.prot_id))
     )

a) Template syntax and the resulting HTML that is generated.

  
 *table.attribute*

        generates a single selection HTML <SELECT>
	pull-down menu,

  
 @table.attribute@

        generates a single selection scrollable 
        <SELECT>	window,
 
  
 @table.attribute@+

        generates a MULTILIST selection scrollable 
        <SELECT> window,

  
 #table.attribute# 

       generates a scrollable non-selectable HTML 
       <TEXTAREA> window for reviewing data.



b) Menu generation modifiers may be used for additional
   functionality. Let ? be one of the above menu type
   indicators (i.e. *, @, or #).

  
 ! appended in the ?table.attribute?!
	syntax sorts 
       the <OPTION> entries by the most recent RDBMS
       edit_date for that table's entries.  The alternate 
       form !"sortTable.sortAttribute" will sort it by a 
       different entry.

  
 ="new-name" used in the
      ?table.attribute?="new-name" syntax specifies the 
      NAME field with NAME="new-name" instead of the 
      default NAME="table.attribute" in the <SELECT> 
      statement. This syntax allows using several copies of 
      the same menu for different purposes in the same form.