Corporate Banner
Satellite Banner
Scientific Community
Become a Member | Sign in
Home>News>This Article

ATARiS Informatics Platform Hits the Jackpot

Published: Wednesday, May 22, 2013
Last Updated: Wednesday, May 22, 2013
Bookmark and Share
ATARiS is one of several tools developed at the Broad Institute to precisely tune in to the signals within noisy datasets.

Listening to data isn’t easy. Massive amounts of data are often messy and complicated. But somewhere within the cacophony, information can harmonize and produce the sweet sound of discovery – if you have the right tools with which to hear it.

ATARiS is one of several tools developed at the Broad Institute to precisely tune in to the signals within datasets. The original idea for ATARiS came about a few years ago when members of Jill Mesirov’s computational biology and bioinformatics group, Bill Hahn's cancer biology group, and the Broad RNAi Platform were trying to address a common problem from the world of RNAi research. RNAi – short for RNA interference – allows researchers to “turn off” a gene or decrease that gene’s activity. Ideally, every gene in the genome would be paired with an RNAi reagent that could turn it – and only it – off. Instead, most RNAi reagents also disrupt other genes (a frustrating phenomenon known as off-target effects). Without a way to easily isolate on-target effects, the power of RNAi wanes.

RNAi is a critical tool for many projects at the Broad and beyond, including Project Achilles. This project – a joint effort between researchers at the Dana-Farber Cancer Institute and the Broad – seeks to pinpoint cancer’s most important weaknesses. To do so, researchers use RNAi to turn off genes in hundreds of cell lines. About 50,000 RNAi reagents have been used to target 11,000 of the 21,000 human genes (about five RNAi reagents for each of these genes) in order to see which genes are critical for cancer’s survival. These crucial genes could become the targets of drugs in the future.

“What we want to do is tune in on a specific target effect,” says Diane Shao, a graduate student in senior associate member Bill Hahn’s lab at the Broad Institute and Dana-Farber Cancer Institute. However, while researchers can pick out an RNAi reagent that seems particularly adept at killing cancer cells, they can’t be entirely certain which of its effects – on-target or off-target – are bringing about the desired result.

ATARiS helps cut through the noise from the multitude of variables and values. The computational method looks for patterns across multiple samples, assessing the performance of individual RNAi reagents to target specific genes. This allows researchers to determine which gene – rather than which RNAi reagent – is most of interest.

“ATARiS makes RNAi data more accessible,” says Aviad Tsherniak, a computational biologist in Jill Mesirov’s lab at the Broad and the key architect of ATARiS. “It simplifies it and standardizes it, and it makes the data compatible with other kinds methods.”

Further Information
Access to this exclusive content is for Technology Networks Premium members only.

Join Technology Networks Premium for free access to:

  • Exclusive articles
  • Presentations from international conferences
  • Over 2,800+ scientific posters on ePosters
  • More than 4,000+ scientific videos on LabTube
  • 35 community eNewsletters

Sign In

Forgotten your details? Click Here
If you are not a member you can join here

*Please note: By logging into you agree to accept the use of cookies. To find out more about the cookies we use and how to delete them, see our privacy policy.

Related Content

Screen of Human Genome Reveals Set of Genes Essential for Cellular Viability
Using two complementary analytical approaches, scientists at Whitehead Institute and Broad Institute of MIT and Harvard have for the first time identified the universe of genes in the human genome essential for the survival and proliferation of human cell lines or cultured human cells.
Monday, October 19, 2015
GTEx: Useful Expression For Cancer Research
GTEx Project has recently published several papers reporting on findings from its two-year pilot phase.
Tuesday, May 26, 2015
In vivo CRISPR-Cas9 Screen Sheds Light On Cancer Metastasis And Tumor Evolution
Genome-scale study points to drivers of tumor evolution and metastasis, provides roadmap for future in vivo Cas9 screens.
Friday, March 06, 2015
Disorder in Gene-Control System is a Defining Characteristic of Cancer, Study Finds
Findings indicate that the disarray in the on-off mechanism is one of the defining characteristics of cancer.
Tuesday, December 23, 2014
Two Studies Identify A Detectable, Pre-Cancerous State In The Blood
Findings pave way for new lines of cancer research focused on detection and prevention.
Thursday, November 27, 2014
Dramatic Response And Resistance To Cancer Drug Traced
Sequencing reveals why thyroid tumor responded to, and eventually resisted, treatment.
Friday, October 10, 2014
Study Expands the Cancer Genomics Universe
The universe of cancer mutations is much bigger than previously thought, and key cancer genes are still to be discovered.
Tuesday, January 28, 2014
Predicting Cancer’s Next Move
Research offers a new approach to studying drug resistance in cancer.
Monday, November 11, 2013
Study Finds Rules for Cancer Drivers
Any number of alterations to an individual’s genetic code has the potential to make a cell malfunction and proliferate into cancer tumors.
Monday, September 30, 2013
Broad Institute and Bayer Join Forces
The Broad Institute has entered into a strategic alliance with Bayer Healthcare in the area of oncogenomics and drug discovery.
Wednesday, September 11, 2013
Bringing Out the Usual – and Unusual – Cancer Genomics Suspects
Several years ago, researchers sequencing lung cancer genomes encountered a number of red herrings.
Tuesday, June 18, 2013
Chemical Screen Points to New Line of Attack Against Neuroblastoma
In the war on neuroblastoma, the current chemical weaponry is reaching its limit.
Monday, June 10, 2013
Researchers Unearth New Clues About How Prostate Cancer Evolved
With the help of a computational model, Broad researchers were able to reconstruct the genomes of prostate cancer cells.
Thursday, May 16, 2013
Endometrial Cancer Findings Emerge from Genome Sequencing Study
Novel tumor sub-types have been identified that could lead to better risk stratification and more individualized and targeted treatments.
Friday, May 10, 2013
Delivering on a Promise: Nanoparticles Carry siRNA to Tumours
RNA interference, a gene-silencing phenomenon discovered in the late 1990s, was hailed for its potential as a treatment in cancer and other diseases.
Friday, September 21, 2012
Scientific News
Nanocarriers May Carry New Hope for Brain Cancer Therapy
Berkeley lab researchers develop nanoparticles that can carry therapeutics across the brain blood barrier.
RNA-Based Drugs Give More Control Over Gene Editing
CRISPR/Cas9 gene editing technique can be transiently activated and inactivated using RNA-based drugs, giving researchers more precise control in correcting and inactivating genes.
University of Glasgow Researchers Make An Impact in 60 Seconds
Early-career researchers were invited to submit an engaging, dynamic and compelling 60 second video illuminating an aspect of their research.
Metabolic Profiles Distinguish Early Stage Ovarian Cancer with Unprecedented Accuracy
Studying blood serum compounds of different molecular weights has led scientists to a set of biomarkers that may enable development of a highly accurate screening test for early-stage ovarian cancer.
Dead Bacteria to Kill Colorectal Cancer
Scientists from Nanyang Technological University (NTU Singapore) have successfully used dead bacteria to kill colorectal cancer cells.
CRISPR-Cas9 Gene Editing: Check Three Times, Cut Once
Two new studies from UC Berkeley should give scientists who use CRISPR-Cas9 for genome engineering greater confidence that they won’t inadvertently edit the wrong DNA.
Genetically Engineering Algae to Kill Cancer Cells
New interdisciplinary research has revealed the frontline role tiny algae could play in the battle against cancer, through the innovative use of nanotechnology.
How to Control Shape, Structure of DNA and RNA
Researchers have used computational modelling to shed light on precisely how charged gold nanoparticles influence the structure of DNA and RNA.
Advancing Genome Editing of Blood Stem Cells
Genome editing techniques for blood stem cells just got better, thanks to a team of researchers at USC and Sangamo BioSciences.
Gene-Edited Immune Cells Treat ‘Incurable’ Leukaemia
A new treatment that uses ‘molecular scissors’ to edit genes and create designer immune cells programmed to hunt out and kill drug resistant leukaemia has been used at Great Ormond Street Hospital (GOSH).

Skyscraper Banner
Go to LabTube
Go to eposters
Access to the latest scientific news
Exclusive articles
Upload and share your posters on ePosters
Latest presentations and webinars
View a library of 1,800+ scientific and medical posters
2,800+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
4,000+ scientific videos