Big Data Tool to Reveal Immune System Role in Diseases
Researchers from the Icahn School of Medicine at Mount Sinai and Princeton University have designed a new online tool that predicts the role of key proteins and genes in diseases of the human immune system. Called “ImmuNet,” details of the publically available resource were published online today in the journal Immunity.
The tool uses information compiled from 38,088 public experiments to predict new immune pathway interactions, mechanisms, and disease-associated genes. With advances in inexpensive computing power, and stored data collections becoming massive in the era of “big data,” researchers are now able to combine algorithms and models into tools like ImmuNet that pull previously unrecognized disease patterns from databases. These computational patterns are predictive, and researchers can test them with further experiments.
“This new tool unlocks the insight contained in big data, the world’s biomedical research output, to help understand immunological mechanisms and diseases,” said Stuart Sealfon, MD, Chairman and Glickenhaus Professor, Department of Neurology, Mount Sinai Health System and co-senior author of the publication. “The goal of ‘ImmuNet’ is to accelerate the understanding of immune pathways and genes, ultimately leading to the development of improved treatment for diseases with an immunological component.”
ImmuNet enables immunology researchers without special computational training to use the statistical techniques of Bayesian data integration and machine learning algorithms to “interrogate” this huge compendium of public data. Bayesian analysis is able to detect relevant information in a sea of often conflicting data obtained from diverse experiments. This form of analysis selects only the datasets that provide new insight about a pathway of interest while excluding datasets that are not relevant to the targeted pathway.
A goal of the online tool is to advance the understanding of the immune system, the network of cells and organs that protects the body against infections and cancer. While the immunity protects against infection, immune cells may also target the body’s own cells to cause inflammation as part of many diseases where the mechanisms are not yet known.
“We expect the applicability of ImmuNet to wide ranging areas of immunology will grow with the incorporation of continually increasing public big data,” said Olga Troyanskaya, PhD, Professor, Department of Computer Science and Lewis-Sigler Institute of Integrative Genomics, Princeton University and Deputy Director of Genomics, Simons Center for Data Analysis, co-senior author of the publication. “By enabling immune researchers from diverse backgrounds to leverage these valuable and heterogeneous data collections, ImmuNet has the potential to accelerate discovery in immunology.”
This development of the online resource was funded by a grant (contract # HHSN272201000054C) from the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health. Co-collaborators of the study include researchers from Yale University, New York Genome Center, and the Simons Center for Data Analysis.
About the Mount Sinai Health System
The Mount Sinai Health System is an integrated health system committed to providing distinguished care, conducting transformative research, and advancing biomedical education. Structured around seven hospital campuses and a single medical school, the Health System has an extensive ambulatory network and a range of inpatient and outpatient services—from community-based facilities to tertiary and quaternary care.
The System includes approximately 7,100 primary and specialty care physicians; 12 joint-venture ambulatory surgery centers; more than 140 ambulatory practices throughout the five boroughs of New York City, Westchester, Long Island, and Florida; and 31 affiliated community health centers. Physicians are affiliated with the renowned Icahn School of Medicine at Mount Sinai, which is ranked among the highest in the nation in National Institutes of Health funding per investigator. The Mount Sinai Hospital is in the "Honor Roll" of best hospitals in America, ranked No. 15 nationally in the 2016-2017 "Best Hospitals" issue of U.S. News & World Report. The Mount Sinai Hospital is also ranked as one of the nation's top 20 hospitals in Geriatrics, Gastroenterology/GI Surgery, Cardiology/Heart Surgery, Diabetes/Endocrinology, Nephrology, Neurology/Neurosurgery, and Ear, Nose & Throat, and is in the top 50 in four other specialties. New York Eye and Ear Infirmary of Mount Sinai is ranked No. 10 nationally for Ophthalmology, while Mount Sinai Beth Israel, Mount Sinai St. Luke's, and Mount Sinai West are ranked regionally. Mount Sinai's Kravis Children's Hospital is ranked in seven out of ten pediatric specialties by U.S. News & World Report in "Best Children's Hospitals."