Allow users to view complex survival analyses for multiple cancers in a single click.
OncoLnc is the simplest and most extensive tool available for viewing survival analyses of your gene of interest.
A factual abstract
OncoLnc was created out my frustration with the current tools available for correlating TCGA survival data with gene expression. It should be possible to not only explore the correlation to survival of your gene of interest, but also possible to get a sense of the strength of the correlation compared to other genes.
With a current tool you might be able to find that the expression of your gene correlates to time to death with a p-value below .05 in a specific cancer, but does that mean your gene is in the top 1% of correlated genes, top 10%, top 50%? And what about other cancers?
OncoLnc contains the results for over 400,000 multivariate Cox regressions. Each model was carefully generated for each cancer and data type (mRNAs, miRNAs, lncRNAs), and the results of each model for your gene of interest can be viewed in a single click.
OncoLnc also allows the user to perform further analysis with interactive Kaplan-Meier plot generation and allows for convenient download of data. OncoLnc is the only online tool that gives users full control over dividing patients by expression, and the only place where you can download expression data coupled to survival data.
With OncoLnc researchers can identify potential tumor suppressors and oncogenes with unprecedented ease and accuracy.
The story behind the paper
As a MD/PhD student I had an interest in the growing field of genomics and the exponentially increasing capabilities of technology, and was drawn to projects that utilized large data sets and new bioinformatics tools. However, my department did not appreciate computational work and I was discouraged from pursuing these types of projects, and I was told by my department that I was not allowed perform my proposed thesis work. Despite having been in the MD/PhD program for 4 years, and having completed all course and publication requirements for my PhD, I decided to leave the program to give myself the freedom to perform the work I was interested in.
When I left I had knowledge of Python programming, but I had no knowledge of web development and began taking online courses in order to give myself the ability to share my work. As soon as I knew enough web development to make a basic site I launched omnesres.com, where I make my research and code freely available, and also offer much needed services to researchers.
I was interested in seeing if I was capable of making more complicated websites, and had a lot of experience working with TCGA data, so I decided to try and make a TCGA data portal. It turns out that with the web frameworks and online tutorials available today, it is not that difficult to make a dynamic site, but OncoLnc stores a large amount of data and my initial versions took too long to query the database. After many sleepless nights and increasingly more complex database structures, I eventually managed to get the query speed to acceptable levels.
Although it may seem crazy to leave a career as a MD/PhD, if I didn’t leave the program I never would have created OncoLnc and I don’t know how long it would have taken someone to make a comparable tool. I already know researchers writing grants based on results from OncoLnc, and I hope OncoLnc leads to advances in cancer. In addition, the web skills I developed will allow me to create more free tools that help the scientific community.
The complete publication should be cited as:
OncoLnc: Linking TCGA survival data to mRNAs, miRNAs, and lncRNAs
PeerJ PrePrints 4 (2016),e1780
Founder of Omnes Res
I am a strong believer in academic freedom and open science. I was the top graduating science student for UC Berkeley class of 2009, and have made significant contributions to projects in 9 different labs throughout my career. Unhappy with the constraints of my MD/PhD program, I decided to leave the university to give myself the absolute academic freedom which all scientists should be afforded.
To contribute to the open science movement I picked up web development and started sharing my work via various websites and submitting my work to preprint servers. Currently I am working on developing new web tools that will help advance the open science movement.