Usage instructions

1. Specify the input molecules and indications

This web-server prioritizes all genes in the genome for their likelyhood of being involved in pharmacogenetic responses to the inputted drugs and indications. The drugs are inputted as structures and the indications are selected from a list of indications used in the Pharmgenetics and Pharmacogenomics Knowledge Base (PharmGKB).

There are four possible ways of entering molecular structure information:

1. Draw the molecule in the JME window to the right and click on the "Import" buttom to translate to SMILES-format.
2. Insert the SMILES strings of the molecules in the window to the left.
   
3. Read the SMILES strings from a file (*.smi)
   
4. Read the structures from a sdf file (*.sdf) Sample copy

The SMILES entry window and SMILES files should have the following format, where multiple structures can be entered on separate lines:

[SMILES-string]<TAB>[Identifier]

CCOC(=O)C1=CC=C(C=C1)N	Benzocaine
CC(=O)OC1=CC=CC=C1C(=O)O	Aspirin
CCOC(=O)CC(C(=O)OCC)SP(=S)(OC)OC	Malathion
CC12CCC3C(C1CCC2O)CCC4=CC(=O)CCC34C	Testosterone
C1=CC=C(C=C1)C2(C(=O)NC(=O)N2)C3=CC=CC=C3	Phenytoin
C1C2C(C(C1Cl)Cl)C3(C(=C(C2(C3(Cl)Cl)Cl)Cl)Cl)Cl	Chlordane

If identifiers are left out, the molecules will be designated compound1, compound2...

2. Customize your run

You can choose to return only the top-scoring genes by setting the threshold on the logistic score for each gene-drug interaction. The lowest possible score is -2.71, and the best separation of positive and negative gene-drug interactions is obtained for -1.07.

Alternatively, you can choose to return only the top-ranking genes by setting the Max number of genes to a specific value.

3. Submit the job

Click on the "Submit" button. The status of your job (either 'queued' or 'running') will be displayed and constantly updated until it terminates and the server output appears in the browser window.

At any time during the wait you may enter your e-mail address and simply leave the window. Your job will continue; you will be notified by e-mail when it has terminated. The e-mail message will contain the URL under which the results are stored; they will remain on the server for 24 hours for you to collect them.