Help - How to use the RCCL Collection Database
The search page offers multiple options to explore and analyse the data present in the RCCL Collection Database. The options are explained below
See all drug sensitivity data for a particular drugThe search page drug table is shown below. It lists the most widely tested drugs in the database . Each drug name links to page displaying details about the drug and drug sensitivity data for all the cell lines that it has been tested on.
|Platinum drugs||Alkylating agents||Topoisomerase I inhibitors||Topoisomerase II inhibitors||Tubululin-binding agents||Kinase inhibitors||Anti-metabolites||Others|
Performing more specific searchesOn the search page five different search options are displayed. They enable more complex searches of the database than the single drug selection. The options for each search are hidden by default, click "Show/Hide search options" to display the form. All search options have buttons to select if parental (i.e. non drug adapted cell lines) and drug adapted cell lines are returned, both are selected by default. One of these options can be unselected if you only want to see data from parental or drug adapted cell lines.
1. See all dataThe first search option simply returns all of the data in the RCCL database. This enables the user to browse the data. By default only a table of the result are displayed. A link at the bottom of the page enables the results to be displayed with a bar chart for each drug tested, which is not shown by default as it can take a few minutes to render.
2. Search for data from a set of cell linesThe second search option enables users to see drug sensitivity data obtained for two or more cell lines. Simply select the cell lines of interest in the box displayed.
3. Search for data for a type of cancerThe third search option enables users to see drug sensitivity data for cell lines from one or selected cancer type. Simply select the cancer type(s) of interest in the box displayed.
4. Search for data testing cell line sensitivity to specific drugsThe fourth search option enables users to see drug sensitivity data for specific drugs. Simply select the drug(s) of interest in the box displayed.
5. Compare Drug sensitivity between two or more cell linesThe fifth search option enables users to compare drug sensitivity data between multiple cell lines. Simply select the cell lines that you would like to compare from the box displayed.
Individual Drug PagesWhen users have searched for an individual drug (i.e. select a drug from the drug table shown on the search page) the results page first displays informaiton about the drug, as shown for carboplatin below. Much of this information is extracted from Wikipedia. It shows the structure of the drug, clinical data associated with the drug, information on pharmacokinetics and also identifiers for databases that contain information about the drug. Many of the values displayed are links to the availabel data from that resource on the drug.
The Carboplatin information table
The results tableAll results pages display tables containing the returned drug sensitivity data. An example table is shown below for the drug Carboplatin in a selection of cell lines The columns contain the data as set out below. For the final four columns data is only available for some cell lines, where data is not available for these the cell is left blank
|Cell line name||The name of the cell line that has been used|
|Cancer Type||The type of cancer that the cell line originates from|
|Parental cell line||For drug adapted cell lines the name of the parental cell line is displayed|
|Drug adapted to||For drug adapted cell lines the name of the drug the cell line has been adapted to|
|Drug tested||The name of the drug that sensitivity of the cell line has been tested|
|IC50 of drug tested||The IC50 for the drug tested|
|IC90||The IC50 for the drug tested|
|ABCB1 status||The status of the ABCB1 expression + indicates overexpression of the gene.|
|ABCC1 status||The status of the ABCC1 expression + indicates overexpression of the gene.|
|p53 status||The name of the cell line that has been used|
An example drug sensitivty table for Carboplatin sensitivity
This table shows drug sensitivity data to carboplatin for the neuroblastoma cell line UKF-NB-3 and drug adapted sub-lines. Data is available for sublines adapted to Cisplatin, Carboplatin, Dacarbazine, Docetaxel, Etoposide, Gemcitabine, Melphalan, Oxaliplatin, Topotecan, vinblastine and Vincristine, as shown in the "drug adapted to" column
Drug sensitivity barchartsTwo types of barcharts are plotted on different results pages, examples are shown below. The first shows data when sensitivity to a single drug is being displayed. The second type is used when drug sensitivty to multiple drugs is considered. Both charts are interactive, for example moving the mouse over a column will indicate the name name of the cell line and the IC50 value.
Barchart displaying drug sensitivity to a single drug
The barchart above shows the same data as the example table. In this display, parental cell lines are shown in darker colours (in this case UKF-NB-3) The chart shows that some of the adapted sublines are resistant to carboplatin compared to the parental UKF-NB-3 cell line. Interestingly the cisplatin adapted subline (UKF-NB-3rCDDP) is much more resistant to carboplatin that the carobplatin adapted subline (UKF-NB-3rCARBO). Data in this form enables consideration or cross resistance, which can provide insights into mechanisms of drug resistance, mechanisms of drug action, and suitablity of next line therapies. The barchart shows the drug sensitivity (IC50) to both Carboplatin and Cisplatin for the same set of cell lines as in the previous example. In this format the key on the right of the graph sets out the colouring of the cell lines.
Comparing drug sensitivity between multiple cell linesThe fifth search option enables comparison of drug sensitivity between a set of cell lines. Where three or more cell lines the data is displayed using a combination of tables and barcharts of a similar format to those above. When only two cell lines are directly compared the data is also displayed as a scatter graph as shown below.
Scatter graph to compare drug sensitivity between cell lines