Does your gene drug target have other implications? Enter: MORPHIN

MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network.

If you missed it, there was another headline reporting the discovery of a new potential gene target, “CREB3L3 May Be Target for Obesity, Diabetes Treatments” that has shown promise in mice anyway. In light of all these new disease-related genes being discovered daily–in various model organisms–wouldn’t it be awesome if there was a tool that allowed us see how new genes discovered in model organisms linked to human disease? This may seem like a strange thing to do considering the fact that researchers use model organisms in order to study human diseases in the first place. After all, one would expect that the genes discovered in a model organism whilst conducting research on a particular disease should link to the disease being modeled, right? Of course! But what if the gene you discover while researching angina actually plays a big role in erectile dysfunction? What if the gene you’re targeting for erectile dysfunction may actually play an important role in muscular dystrophy? While Viagra was originally developed to treat angina by targeting phosphodiesterase 5, it became a blockbuster treatment for erectile dysfunction. Similarly, Cialis which was developed also targeting PDE5 for erectile dysfunction has been explored for the treatment of Beckman’s muscular dystrophy.

Research behind the little blue pill started with angina. By Tim.Reckmann (Own work) [CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0)%5D, via Wikimedia Commons

The point is…maybe you’ve uncovered a group of genes that may be the key to a disease you’re studying, but there may be other disease indications you may want to consider branching off and studying in the future. And now, there’s a tool to help with that: Enter MORPHIN

I tested MORPHIN using the gene from the aforementioned article: CREB3L3, along with another gene that has been hyped as a target for curing obesity: Leptin (LEP) and the Leptin receptor (LEPR). I entered the three genes, selected ‘mouse’ for the model, and submitted the query.

Unfortunately, MORPHIN is very slow. A query can take 3-5 min, even 20 min if there’s a queue. I’m guessing the delays stems from using not an overlap-based gene set association measure (Fisher exact test) in addition to a network-based gene set association measure, RIDDLE to enhance the sensitivity of association mapping. RIDDLE itself takes 2-3 min to run if you’re lucky. I’m sure the mapping of queried animal genes to human orthologs is the fastest part considering there are really fast services already available like http://mygene.info.

35 min later, we have the result! (MORPHIN must be really popular!). Of course, the first disease that was associated with these three genes was ‘Eating disorders.’ The second one was ‘HELLP syndrome’. A quick search in pubmed reveals that there are 2000+ articles on HELLP syndrome, four of which are linked to Leptin, none to CREB3L3. Interesting. Might be fun to try and see how the results of a query for various phosphodiesterases, but I don’t think I can spare another hour on this.

If you’re curious, see the development time line of Viagra here.

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Surrounded by geniuses- part 7 : Adam

adam matrix copy The Mysterious Genius of the Su Lab remained quite the mystery even after I’d been with the lab for a month. Where did he come from? Where does he vanish to? What is he working on? Given the extremely varied backgrounds of the other Su lab members, it would make sense if he was a member of a secret organization dedicated to liberating humans from machines hellbent on enslaving humanity. Were this the case…did I really write this post?

Fortunately, the Mysterious Genius, Adam Mark, doesn’t appear from and disappear into a higher plane of reality. He’s just making the painful commute between the Su lab at TSRI and San Diego State University, where he just completed his first year as an M.S. Candidate in Biomedical Informatics.

Enthusiastic about both bench work and programming, Adam would love to combine his two disparate skill sets to transcend the translational genomics and big data realm. The Mysterious Genius has been working on developing an R client for MyGene.info as well as MyVariant.info.

Excellent!
Don’t be fooled by the surfer dude vibe…Adam is unmistakably intelligent
An avid surfer and genuine connoisseur of ocean waves, the Mysterious Genius has traveled throughout Asia and the south pacific, and plans to make a trip to the Meditarranean soon. Not so mysterious, after all? Think again! The Mysterious Genius seems to be a beach-loving, wave-surfing, fun-in-the-sun, kind of genius, but further investigations reveal a colder, darker side to him.
 
Duck!!!
Forget the hockey coach scouting Adam for his team, Adam became a coach himself
Throughout his undergrad, he played for SDSU’s ice hockey team and then went on to coach the sport for two years after graduating. After graduating, with a B.S. in biochemistry, Mysterious Genius joined Dr. Saloman’s lab at TSRI and even contributed to a publication in the prestigious journal, Science. Upon returning to SDSU for graduate studies, Mysterious Genius was recruited by the genius-in-charge with insane mental organizational skills to conduct his thesis research in Biomedical Informatics.