MDP Help

Introduction

MDP is a web tool able to investigate the complete data provided by the National Cancer Institute's anticancer drug screen data (DTP NCI60) and the Cancer Cell Line Encyclopedia (CCLE) starting from a single or a pool of mutations/genes linked to the compounds that show a statistical significant anticancer activiy.
MDP is also able to investigate this collection of data starting from a singles drug, in order to provide as a result a list of mutations that are statistically correlated with the investigated drug.
The tool works by typing one or more Gene Names or Mutations or a single Drug, that are included in the NCI60 or CCLE databases respectively.

Analysis

MDP is structured to perform two different set of analysis and each one can be conducted either on the NCI60 dataset or on the CCLE dataset, for a total of four kind of analysis.
These two analysis are termed "From Gene to Drug" when the starting input is one or more Gene/Mutation (via SNP ID) and "From Drug to Gene" when the starting input is a Drug name.

Workflow

After the selection of one or more gene(s)/mutation(s), the tool will ask for the tissue(s) of interest.
More than one tissue can be selected at once, simply by clicking in the related checkbox.
You may notice that changes in the searched gene/mutation will lead to a wider or smaller pool of tissues.
MDP automatically shows only tissues available for the running search, filtering out those features that are not consistent with the gene(s) or mutation(s) selected.
The next step in MDP is the selection of the different type of mutation to be searched for. As stated for the selection of tissues, MDP is able to run the analysis used only the type of mutations selected. You can also investigate for the mutations correlated to a single drug. In this case, after the selection of the drug to be investigated, no other steps or parameters will be required in order to perform the analysis

Output

A search recap with the selected paramaters during the wizard is then showed before running the procedure. By clicking the “Proceed” button, MDP will start the analysis. Calculations will output a complete web page with plots, barplots and an interactive table with the most active compounds sorted for their score and p-value. Score values range from 0 to 1. P-value for each compound are also reported in the interactive output table. When P-value are less or equal to ~0.05 are highlighted in blue.
This table may be investigated both online and offline, by downloading the related Excel file.