Why is it called DORM?
DORM lists the recurrent mutations (i.e. mutations with population frequency > 1) idenfied from genomes of cancer samples, therefore it's called Database Of Recurrent Mutations, which we refer internally with the acronym DORM.
How do I save the graphs?
You have 2 options, depending on your use case. a) Take a screenshot. b) Right click (Control-click on a Mac) and then click “Save image”.
Bonus Tip: All the charts are dynamically-generated, so just resize your browser to get the graph in your desired size.
How do I download the table?
At the moment we do not have a “download” button for exporting the table. You have 2 options:
1) Excel: Select the records you want to save, and Copy them. Open an Excel sheet, and Paste the records and then save the file as ".xlsx".
2) PDF: Save the entire webpage as a PDF. e.g. On Safari (Mac), click “File” from the menubar at the top and then click “Export as PDF”. You can Print/Save the webpage as a PDF in other browsers like Chrome, Firefox, etc.
Can I search for more than one protein?
Yes, absolutely! Just string along your proteins or mutations of interest and use either a comma or a semicolon as the delimiter “
EGFR, KRAS; BRAF”. Adding spaces after the comma/semicolon does not affect your search query.
You can also craft advanced search queries using regular expressions. Read more here.
N.B. Blank space is the reserved separator between protein names and mutations, e.g. EGFR L858R, KRAS G12, etc. therefore it cannot be used to separate protein names.
Can I browse your source code?
Yes the code is available on Github. Please report any issues with the tools and your search queries and experience on our separate Issues page here. Links to our code repos: Database generation, DORM - Mutations, and DORM - Residues.
I want to deploy my own instance, is it open-source?
Keeping the framework open-source is one of our key goals. Just clone our github repositories (mentioned above) to process the lates COSMIC data release and host the derived & database on your server. You just need to set up, R along with shiny and a few other R packages (the R code automatically installs the dependencies, incl. shiny). Additionally, to serve the database over the secured HTTPS protocol you can follow this article.
Why are the sample counts on DORM often smaller than what is reported in COSMIC?
COSMIC reports all sorts of detections of cancer-associated somatic mutations from sequencing efforts of all scales, ranging from genome-wide to single gene profiling. Our goal with DORM is to present a holistic view of the Mutational landscape of Cancer. This allows us to present the mutation frequency of all mutations in a better context which is free of any selection-bias.
What information do you collect about my queries?
We do not collect any information about your search queries. Only when you click the Generate link button, your search term(s) and settings are stored on our server anonymously. We never store your search results. The search results are wiped from our disks as soon as they are displayed on your screen. You don’t have to take our word for it, you can check our code at the repositories mentioned above in FAQ #5 .
Can you save my search results?
No, currently we do not offer saving the search results to our servers as we are not offering personal user accounts. However, you can generate a direct link to your search query (see more details in FAQ #10). To download/save the results to your computer refer to FAQ #2 and FAQ #3.
How can I share my search results?
Clicking the "Generate Link" button (under the search bar), shows a direct link to your search query and settings. Copy and save this link.
Your search term(s), selected tissue, displayed number of records, etc. is saved anonymously (i.e. no identifiable information is stored) on our server. When this link is clicked/used again in a browser, it triggers a new search with the exact search parameters.
You can share the link with your colleagues, and it will work for them in the same manner. These links are agnostic to the updates made to our underlying database.
I found interesting results, but I want more information about the samples and the original studies. What do I do?
For further in-depth investigation of your mutations of interest we recommend visiting COSMIC or cBioPortal and manually exploring the data. If you have exciting ideas and would like to collaborate, don’t hesitate to contact us.
Last modified on December 16, 2021.