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Single drug ranking process generally takes several minutes. Combinatorial drug raking takes couple of hours since there are more than one million drug pairs to calculate.
Pathway analysis
Pathway network Links to pathway analysis result page.
This is very important!!! The result page gives you a list of pathways showing similar expression patterns. To deeply understand it, we recommend you to draw a map of the chemicals and genes in these pathways using phExplorer. It gives you a wonderful network view, and a new way for drug repositioning by drawing an integrated relation map.


Advanced search - Set the range of enrichment score
Enrichment score represent the similarity between input gene signatures and reference molecule-treated expression data. The range of score is from 1 to -1. The score “1” means their expression patterns are showing great similarity (positive match). On the other hand, the score “-1” means their patterns are opposite. Up/down input gene signatures are found on down/up raking in reference expression data (negative match). As the score “0” means there is no significant expression pattern similarity, the pathways with this are not included in counting. The default threshold for single drug and combinatorial drug are 0 and 0.5, respectively.
However users can set the range of enrichment score.
eg) Range 0.5~1: Positive Pathways only which satisfy that range.
eg) Range -1~-0.5: Negative Pathways only which satisfy that range.


Chemical detail
Click on the name of chemical to see the details. It is likened to ChemBank.


Count of Positive/Negative
Expression patterns of reference molecule-treated expression data and input signatures can be positively/negatively matched in specific signaling pathways. We counted the number of such pathways to ranking the drugs. As the number of positive match goes up and the number of negative match goes down, we can assume that the functional action of the chemical is more similar to the action of the input.


Positive/Negative Pathways
It the lists of signaling pathways satisfied the range of enrichment score.


Analysis detail
In reference data, a molecule has several instances. Molecules were selectively applied to five different human cancer cell lines (MCF7 and ssMCF7: breast cancer, PC3: prostate cancer, HL60: leukemia, SKMEL: melanoma) for short duration with different doses. By clicking “Detail” button, you can see additional information of instances as well as connectivity scores of them which leads to the enrichment score. Instances are ordered in descending order of connectivity score, and raking represents it.
analysis detail


Network browsing on phExplorer
phExplorer is a visualization network tool. It was for an integrated drug-protein-disease tripartite database called PharmDB which we constructed. Now we integrated these two with CDA to provide much more enrich information. CDA recommend single and combinatorial drugs based on expression of signaling pathway gene sets. However we don’t know whether any genes in these gene sets are related with any drugs or diseases. And phExplorer will help you to get clues by scatter the signaling pathway gene sets on browser and see their known relationships with drugs, proteins and disease.
Network_browsing_on_phExplorer