Happy New Year from BioGPS

This year, BioGPS has received 40K more queries than last year, and that’s not even counting this month’s queries!* According to google scholar, the BioGPS paper has been cited 586 of which 143 were publications in 2014. Publications about the default data sets used in BioGPS were cited 4957 times of which 414 citations were from publications this year. The most recent BioGPS application paper about BioGPS and MyGene.info was cited 36 times this year for a total of 51 citations.

Our excellent Gene of the Week writers, Melissa Lau and Kerin Higa have written about 40 different genes spanning a wide range of topics including, but not limited to: Blood-letting, Body Odors, Blood Brain Barrier, Beats, Breast milk, and Blood Type— all while incorporating all sorts of interesting references such as Pliny the Elder, Game of Thrones, King Oyster, the Iran Hostage Crisis, and so much more. As a fan of their works, I look forward to seeing what they come up with next in 2015!

The utility of BioGPS was augmented by the addition of 32 new plugins this year bringing the total BioGPS plugin count to 625 plugins, of which 366 are publicly shared amongst the BioGPS community.

As seen in our featured article series, BioGPS users study a huge variety of interesting and important subjects ranging from immunology and infectious disease (eg- pertussis and juunin virus) to evolution and model organism knowledge base development. BioGPS users conduct important research elucidating genes involved in circadian regulation in the heart or bone development or even the development of lung disease.

In addition to specific genes, BioGPS users study patterns of gene expression such as those which reveal how maternal obesity may affect fetal development, or those which one day could be used to detect patients at high risk of renal transplant rejection or even to determine if alcohol consumption played a role in an airplane accident.

Happy New Year!  Don't drink and drive!
BioGPS users are also investigating the role of alcohol in plane accidents. If you drink, please do it responsibly.

Thank you for using BioGPS and letting us know about your awesome research. We hope you will continue to add new plugins and tell us (and your colleagues) how BioGPS has been incorporated into your research. Happy New Year!

*2014.01.02 edit – December’s usage stats were a record-breaking 101252 queries! This means the total usage in 2014, was 140k queries higher than in 2013.

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Mark2Cure limited testing still ongoing

If you are participating in our limited test (and have had a chance to really try out Mark2Cure), please let us know what you think. Send an email to contact at mark2cure dot org. If you agreed to participate in our limited test, and haven’t had a chance to try out mark2cure yet, please give it a shot and then let us know what you think. We’d really love to know: How many trainings did you complete? Quests? How can we improve?

This post was originally written for Mark2Cure and can be viewed in its entirety here.

Merry XMAS and Happy researching!

Here’s just a small sample of various XMAS-named science things:

  • Xmas-1 – A rather mysterious fruit fly gene which may affect fruit fly reproduction.
  • Christmas disease – AKA haemophilia B was named after the first patient identified with the disease, Stephen Christmas. Clinically appears to be identical with classic haemophilia. It is an x-linked form of haemophilia caused by deficiency of Christmas factor (factor IX)
  • Christmas Factor – AKA Factor IX, entrez geneID: 2158
  • XMAS: An Experiential Approach for Visualization, Analysis, and Exploration of Time Series Microarray Data
  • XMAS The Xymmer+Mystrium+Adetomyrma+Stigmatomma clade of ants

What have I missed?

BioGPS Featured Article – Microarray characterization of gene expression changes in blood during acute ethanol exposure | The Su Lab

BioGPS Featured Article – Microarray characterization of gene expression changes in blood during acute ethanol exposure | The Su Lab.

Just in time for the holiday travel rush, this week’s BioGPS featured article is like something out of CSI, but for the FAA.

Wait a second, did I read that right? The Federal Aviation Administration has a functional genomics team, and they use BioGPS? –AWESOME!

FAA Functional Genomics Team researcher prepping a qRT-PCR run image from: FAA’s site

Turns out, the FAA has more than just a functional genomics team conducting research on all aspects of making flying safer such as:
-Aerospace Medical
-Biochemistry
-Biodynamics
-Bioinformatics
-Cabin Safety
-Environmental Physiology
-Forensic Toxicology
-Radiobiology
-Vision Research

All of which is exciting and intriguing, but before we digress any further, why is the FAA even interested in this topic?

One reason is microbes! Post-mortem microbial fermentation can produce ethanol in a cadaver, making it difficult to determine if the deceased had been drinking or not based solely on blood alcohol levels. In order to help accident investigators distinguish the source of the blood alcohol content, the FAA Functional genomics team profiled gene expression changes in the blood during acute ethanol exposure. This enabled researchers to identify several patterns of gene expression changes related to alcohol consumption as well as potential biomarkers for future investigation. Not only does this have important implications in investigating the cause of plane crashes, it also has enormous potential for verifying whether or not alcohol played a role in other accidents.

Was there drinking or were the microbes just busy?
Was there drinking or were the microbes just busy?

Check out the BioGPS feature here: BioGPS Featured Article – Microarray characterization of gene expression changes in blood during acute ethanol exposure | The Su Lab.

Or, do some flight sleuthing of your own before you travel. The FAA has lots of interesting figures, stats, and other info on their site, here

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.

BioGPS Featured Article – siRNA screen for genes that affect Junin virus entry uncovers voltage-gated calcium channels as a therapeutic target | The Su Lab

BioGPS Featured Article – siRNA screen for genes that affect Junin virus entry uncovers voltage-gated calcium channels as a therapeutic target | The Su Lab.

One might think that all the hype and panic surrounding Ebola in the US would help to raise awareness for infectious diseases closer to home, but many New World hemorrhagic fever viruses remain largely unknown to the public at large. Junin virus is one such arenavirus that has caused hemorrhagic fever outbreaks in Argentina. Fortunately a vaccine has helped to curb the incidence of disease; however, there are few treatment options available once someone is infected with this virus. Hence, it is important to better understand the behavior of the virus in the host from infection to pathogenesis. Better understanding could lead to better treatment options for not just Junin virus, but also related hemorrhagic fever arenaviruses. The researchers behind this paper used and siRNA screen to find genes that affect Junin virus entry into cells and discovered a potential therapeutic target.

Learn more about this paper and the researchers behind it here. Or go read it now ’cause it’s interesting and free!

If you can READ, you CAN HELP

As mentioned in Andrew’s Tedx Talk in this post, one of the grand challenges in scientific research is creating a system where all scientists can can access the knowledge embedded within the entirety of research literature. With such a system, scientists would be able to build the bridges they need to connect ideas across disparate fields of research faster. But how could such a system be built? While computation-based text miners can be fast and automatic, they are rather error-prone as the ability to read remains a uniquely human skill.

Mark2Cure enlists the help of citizen scientists to annotate biomedical literature–in essence allowing biomedical texts to be mined for useful information.

Beta testing starts soon. Join here now to help: http://mark2cure.org.

This post was originally written for Mark2Cure and can be viewed in its entirety here.