Mount Sinai Researchers Develop New Computational Method to Aid Analysis of Gene Expression Experiments
Mount Sinai researchers have developed a new database that will change how scientists identify drug targets and biomarkers.
Researchers from Mount Sinai School of Medicine have developed a new computational method that will help streamline the analysis of gene expression experiments and provide scientists with a better mechanistic understanding of the differences between diseased and normal cells. The new database and software, called ChIP Enrichment Analysis (ChEA), will revolutionize how researchers identify drug targets and biomarkers. Researchers can find the tool online at http://amp.pharm.mssm.edu/lib/chea.jsp. The data are published in Bioinformatics.
Until ChEA was developed, there was no centralized database that integrated results from ChIP-seq and ChIP-chip experiments—two types of experiments used to identify how proteins called transcription factors potentially regulate all genes in humans and mice. The data that results from these types of experiments is substantial and computational biologists have struggled with how to integrate them. Led by Avi Ma’ayan, PhD, Assistant Professor, Pharmacology and Systems Therapeutics, a team at Mount Sinai integrated the results from these experiments, collecting data from more than 100 proteins that bind DNA to regulate gene expression, called transcription factors, into one database.
"Using ChEA, we were able to link these transcription factors to the genes they regulate for the first time," said Dr. Ma’ayan. "Our program allows researchers to identify which proteins are likely responsible for genetic changes that may cause disease. Using our database, researchers will be able to better identify drug targets."
Dr. Ma’ayan’s team tested ChEA in several case studies. One case study looked at two independent publications that found signature sets of genes that indicate whether a breast tumor was benign or malignant. Both studies came up with lists of genes that were biomarkers of each tumor type. However, the list uncovered in one study did not match the list in the other study; in fact, there was very little overlap in the biomarkers discovered in each study. However, when Dr. Ma’ayan entered the two lists into ChEA, he determined that the genes on both lists have the same regulatory protein, which determines the aberrant expression of these biomarker genes.
"Our reanalysis of these two publications verifies the usefulness of this software and database in gaining a better mechanistic understanding of the role transcription factors play in controlling gene expression, and subsequently, the development of disease," said Dr. Ma’ayan.
About The Mount Sinai Medical Center
The Mount Sinai Medical Center encompasses both The Mount Sinai Hospital and Mount Sinai School of Medicine. Established in 1968, Mount Sinai School of Medicine is one of few medical schools embedded in a hospital in the United States. It has more than 3,400 faculty in 32 departments and 15 institutes, and ranks among the top 20 medical schools both in National Institute of Health funding and by U.S. News & World Report. The school received the 2009 Spencer Foreman Award for Outstanding Community Service from the Association of American Medical Colleges.
The Mount Sinai Hospital, founded in 1852, is a 1,171-bed tertiary- and quaternary-care teaching facility and one of the nation’s oldest, largest and most-respected voluntary hospitals. In 2009, U.S. News & World Report ranked The Mount Sinai Hospital among the nation’s top 20 hospitals based on reputation, patient safety, and other patient-care factors. Nearly 60,000 people were treated at Mount Sinai as inpatients last year, and approximately 530,000 outpatient visits took place.
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About the Mount Sinai Health System
The Mount Sinai Health System is New York City's largest integrated delivery system, encompassing eight hospitals, a leading medical school, and a vast network of ambulatory practices throughout the greater New York region. Mount Sinai's vision is to produce the safest care, the highest quality, the highest satisfaction, the best access and the best value of any health system in the nation. The Health System includes approximately 7,480 primary and specialty care physicians; 11 joint-venture ambulatory surgery centers; more than 410 ambulatory practices throughout the five boroughs of New York City, Westchester, Long Island, and Florida; and 31 affiliated community health centers. The Icahn School of Medicine is one of three medical schools that have earned distinction by multiple indicators: ranked in the top 20 by U.S. News & World Report's "Best Medical Schools", aligned with a U.S. News & World Report's "Honor Roll" Hospital, No. 12 in the nation for National Institutes of Health funding, and among the top 10 most innovative research institutions as ranked by the journal Nature in its Nature Innovation Index. This reflects a special level of excellence in education, clinical practice, and research. The Mount Sinai Hospital is ranked No. 18 on U.S. News & World Report's "Honor Roll" of top U.S. hospitals; it is one of the nation's top 20 hospitals in Cardiology/Heart Surgery, Gastroenterology/GI Surgery, Geriatrics, Nephrology, and Neurology/Neurosurgery, and in the top 50 in six other specialties in the 2018-2019 "Best Hospitals" issue. Mount Sinai's Kravis Children's Hospital also is ranked nationally in five out of ten pediatric specialties by U.S. News & World Report. The New York Eye and Ear Infirmary of Mount Sinai is ranked 11th nationally for Ophthalmology and 44th for Ear, Nose, and Throat. Mount Sinai Beth Israel, Mount Sinai St. Luke's, Mount Sinai West, and South Nassau Communities Hospital are ranked regionally.