(Press-News.org) The strategy used by Google to decide which pages are relevant for a search query can also be used to determine which proteins in a patient's cancer are relevant for the disease progression. Researchers from Dresden University of Technology, Germany, have used a modified version of Google's PageRank algorithm to rank about 20,000 proteins by their genetic relevance to the progression of pancreatic cancer. In their study, published in PLoS Computational Biology, they found seven proteins that can help to assess how aggressive a patient's tumor is and guide the clinician to decide if that patient should receive chemotherapy or not.
The researcher's own version of the Google algorithm has been used in this study to find new cancer biomarkers, which are molecules produced by cancer cells. Biomarkers can help to detect cancer earlier in body fluids or directly in the cancer tissue obtained in an operation or biopsy. Finding these biomarkers is often difficult and time consuming. Another problem is that markers found in different studies for the same types of cancer almost never overlap.
This problem has been circumvented using the Google strategy, which takes into account the content of a web page and also how these pages are connected via hyperlinks. With this strategy as the model, the authors made use of the fact that proteins in a cell are connected through a network of physical and regulatory interactions; the 'protein Facebook' so to speak.
"Once we added the network information in our analysis, our biomarkers became more reproducible," said Christof Winter, the paper's first author. Using this network information and the Google Algorithm, a significant overlap was found with an earlier study from the University of North Carolina. There, a connection was made with a protein which can assess aggressiveness in pancreatic cancer.
Although the new biomarkers seem to mark an improvement over currently used diagnostic tools, they are far from perfect and still need to be validated in a larger follow-up study before they can be used in clinical practice. It remains an open problem to turn these insights into novel drugs which slow down cancer progression. A first step in this direction is the group's cooperation with the Dresden-based biotech company RESprotect, who are running a clinical trial on a pancreas cancer drug.
TU Dresden is a leading German university, whose Center for Regenerative Therapies was awarded excellence status in the national excellence initiative. The work was a cooperation between the bioinformatics group of Prof. Dr. Michael Schroeder and the medical groups of Dr. Christian Pilarsky and Prof. Robert Grützmann.
INFORMATION:
FINANCIAL DISCLOSURE: Funding was provided by the Roland Ernst Stiftung für Gesundheitswesen, MeDDrive TU Dresden, the EU project Ponte and the national projects GoOn, Format, and GeneCloud. The funders had no role in study design, data collection and analysis, decision to publish, or preparation
of the manuscript.
COMPETING INTERESTS: The authors have declared that no competing interests exist.
CITATION: Winter C, Kristiansen G, Kersting S, Roy J, Aust D, et al. (2012) Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes. PLoS Comput Biol 8(5): e1002511. doi:10.1371/journal.pcbi.1002511
PLEASE ADD THIS LINK TO THE FREELY AVAILABLE ARTICLE IN ONLINE VERSIONS OF YOUR REPORT (the link will go live when the embargo ends): http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002511
CONTACT:
Christof Winter: (christof.winter@gmx.net)
Michael Schroeder: ms@biotec.tu-dresden.de
Phone: +49 351 463 400 60
Technische Universität Dresden
Deparment of Bioinformatics
Tatzberg 47-51
Dresden, 01307
GERMANY
Disclaimer
This press release refers to an upcoming article in PLoS Computational Biology. The release is provided by journal staff, or by the article authors and/or their institutions. Any opinions expressed in this release or article are the personal views of the journal staff and/or article contributors, and do not necessarily represent the views or policies of PLoS. PLoS expressly disclaims any and all warranties and liability in connection with the information found in the releases and articles and your use of such information.
Media Permissions
PLoS Journals publish under a Creative Commons Attribution License which permits free reuse of all materials published with the article, so long as the work is cited (e.g., Brinkworth RSA, O'Carroll DC (2009) Robust Models for Optic Flow Coding in Natural Scenes Inspired by Insect Biology. PLoS Comput Biol 5(11): e1000555. doi:10.1371/journal.pcbi.1000555). No prior permission is required from the authors or publisher. For queries about the license, please contact the relative journal contact indicated here: http://www.plos.org/about/media-inquiries/embargo-policy/
About PLoS Computational Biology
PLoS Computational Biology features works of exceptional significance that further our understanding of living systems at all scales through the application of computational methods. All works published in PLoS Computational Biology are open access. Everything is immediately available subject only to the condition that the original authorship and source are properly attributed. Copyright is retained.
About the Public Library of Science
The Public Library of Science (PLoS) is a non-profit organization of scientists and physicians committed to making the world's scientific and medical literature a freely available public resource. For more information, visit http://www.plos.org.
END
###
Weill Cornell Medical College
Weill Cornell Medical College, Cornell University's medical school located in New York City, is committed to excellence in research, teaching, patient care and the advancement of the art and science of medicine, locally, nationally and globally. Physicians and scientists of Weill Cornell Medical College are engaged in cutting-edge research from bench to bedside, aimed at unlocking mysteries of the human body in health and sickness and toward developing new treatments and prevention strategies. In its commitment to global health and ...
In two back-to-back reports published online on 17 May in Cell, researchers have sequenced the genomes of 21 breast cancers and analysed the mutations that emerged during the tumours' development. The individual results are described below.
Led by researchers from the Wellcome Trust Sanger Institute, the team created a catalogue of all the mutations in the genomes of the 21 cancer genomes and identified the mutational processes that lead to breast cancer. They found that these mutations accumulate in breast cells over many years, initially rather slowly, but picking up ...
Researchers at the SIB Swiss Institute of Bioinformatics and the EMBL-European Bioinformatics Institute have confirmed the long-held conjecture that studying the genes we share with other animals is a viable means of extrapolating information about human biology. The study, published in the open access journal PLoS Computational Biology, shows how bioinformatics makes it possible to test the conjecture.
Scientists have long looked to model species – mice, for example – to understand human biology. This is at the root of what is called the 'ortholog conjecture': the idea ...
Imagine reading an entire book, but then realizing that your glasses did not allow you to distinguish "g" from "q." What details did you miss?
Geneticists faced a similar problem with the recent discovery of a "sixth nucleotide" in the DNA alphabet. Two modifications of cytosine, one of the four bases that make up DNA, look almost the same but mean different things. But scientists lacked a way of reading DNA, letter by letter, and detecting precisely where these modifications are found in particular tissues or cell types.
Now, a team of scientists from the University ...
VIDEO:
This is an interview with Dr. Panda.
Click here for more information.
LA JOLLA, CA----It turns out that when we eat may be as important as what we eat. Scientists at the Salk Institute for Biological Studies have found that regular eating times and extending the daily fasting period may override the adverse health effects of a high-fat diet and prevent obesity, diabetes and liver disease in mice.
In a paper published May 17 in Cell Metabolism, scientists from Salk's ...
Researchers at the SIB Swiss Institute of Bioinformatics and the EMBL-European Bioinformatics Institute have confirmed the long-held belief that studying the genes we share with other animals is useful. The study, published today in the open access journal PLoS Computational Biology, shows how bioinformatics makes it possible to test the fundamental principles on which life science is built.
Studying genes helps life science researchers understand how our bodies work and how diseases progress. Scientists have long looked to model species – mice, for example – to understand ...
Technology is helping communication companies merge telephone, television and Internet services, but a push to deregulate may leave some customers on the wrong side of the digital divide during this convergence, according to a Penn State telecommunications researcher.
"Moving away from copper lines is an example of abandoning obsolete technology and embracing technology that is faster, better, cheaper and more convenient," said Rob Frieden, Pioneers Chair in Cable Television and professor of telecommunications and law. "But the risk is that we may be creating a digital ...
MADISON – An international team of researchers has discovered how adding trace amounts of water can tremendously speed up chemical reactions—such as hydrogenation and hydrogenolysis—in which hydrogen is one of the reactants, or starting materials.
Led by Manos Mavrikakis, the Paul A. Elfers professor of chemical and biological engineering at the University of Wisconsin-Madison, and Flemming Besenbacher, a professor of physics and astronomy at the University of Aarhus, Denmark, the team published its findings in the May 18 issue of the journal Science.
Hydrogenation ...
For pregnant women, including those who are overweight and obese, following a healthy calorie controlled diet during pregnancy is safe and can reduce the risk of serious complications such as pre-eclampsia, diabetes and premature birth, finds a study published on bmj.com today.
In the UK, more than half the women of reproductive age are overweight or obese, and across Europe and the US, up to 40% of women gain more than the recommended weight in pregnancy. Excessive weight gain during pregnancy is associated with a number of serious health problems.
Pregnancy is thought ...
The recent excesses of Wall Street may be big news but behind the headlines there's another story: When it comes to men and women stockbrokers, someone is taking home a bigger paycheck.
New research shows that women stockbrokers sometimes earn as much as 20 percent less than their male counterparts. "Stockbrokers are among the highest paid workers, yet they have the greatest gender inequality among all sales worker jobs," says Prof. Janice Fanning Madden, who conducted the research.
Her paper "Performance-Support Bias and the Gender Pay Gap Among Stockbrokers," will ...
