Case announces launch of gene expression analysis software

December 17, 2004

Case Western Reserve University has announced that its BAMarrayTM software is now available for download and licensing. The statistical software analyzes gene expression data -- one of the hottest areas of biology research.

Gene expression data is becoming abundant with the popularity of microarrays. Microarrays, or gene chips, allow researchers to simultaneously assess the relative expression of thousands of genes. While this technology produces rich sources of data, the analysis of such data proves troublesome. BAMarray virtually eliminates the time-consuming step of evaluating which genes are affected by an experiment and require further study.

BAMarray analyzes the genomic data extracted from microarrays and produces lists of genes that show biologically interesting expression profiles across experimental groups. The software provides both diagnostic and inferential graphical plots to help users better understand their data. The user can interactively view, zoom in, label, and generate lists of color coded genes that were significantly up-regulated or down-regulated.

Sanford Markowitz, M.D., the Ingall Professor of Cancer Genetics at the Case Western Reserve University School of Medicine and University Hospitals of Cleveland and an investigator with the Howard Hughes Medical Institute, searches for the genes involved in the development of colon cancer and has incorporated BAM into his research. He said, "BAM technology allows us to find genes with important expression changes in colon cancer that we could not have found using other approaches."

BAMarrayTM software incorporates the Bayesian Analysis of Variance for Microarrays (BAM) methodology developed jointly at the Case and Cleveland Clinic Foundation Departments of Biostatistics and Epidemiology by J. Sunil Rao of Case and Hemant Ishwaran of the Cleveland Clinic Foundation. The methodology relies on a special type of inferential regularization that allows it to find more truly differentially expressing genes.

"The technique allows researchers to discover statistically significant genes from gene chip experiments that are normally hidden in statistical noise," said Ishwaran.

"Researchers here at Case have already found our methodology useful," said Rao. "We are thrilled that this software is now available to scientists everywhere."

"We've positioned this software for quick distribution and ease of use," said Ian Spatz, the case manager in the Case Technology Transfer Office responsible for the project. "I fully expect significant discoveries to be made using this powerful tool."

Joe Jankowski, assistant vice-president for biomedical sciences, added "This software is a great example of in-house technology validation. With Case's support, Rao and Ishwaran have been able to make a complex analysis technique simple and easy to use."
More information on the software is available on the BAM Homepage at BAMarrayTM Software can be downloaded from BAMarrayTM uses a friendly Java interface. Version 1.0 is available for commercial licensing or free academic licensing (version 2.0 will be coming very soon).

Case Western Reserve University

Related Data Articles from Brightsurf:

Keep the data coming
A continuous data supply ensures data-intensive simulations can run at maximum speed.

Astronomers are bulging with data
For the first time, over 250 million stars in our galaxy's bulge have been surveyed in near-ultraviolet, optical, and near-infrared light, opening the door for astronomers to reexamine key questions about the Milky Way's formation and history.

Novel method for measuring spatial dependencies turns less data into more data
Researcher makes 'little data' act big through, the application of mathematical techniques normally used for time-series, to spatial processes.

Ups and downs in COVID-19 data may be caused by data reporting practices
As data accumulates on COVID-19 cases and deaths, researchers have observed patterns of peaks and valleys that repeat on a near-weekly basis.

Data centers use less energy than you think
Using the most detailed model to date of global data center energy use, researchers found that massive efficiency gains by data centers have kept energy use roughly flat over the past decade.

Storing data in music
Researchers at ETH Zurich have developed a technique for embedding data in music and transmitting it to a smartphone.

Life data economics: calling for new models to assess the value of human data
After the collapse of the blockchain bubble a number of research organisations are developing platforms to enable individual ownership of life data and establish the data valuation and pricing models.

Geoscience data group urges all scientific disciplines to make data open and accessible
Institutions, science funders, data repositories, publishers, researchers and scientific societies from all scientific disciplines must work together to ensure all scientific data are easy to find, access and use, according to a new commentary in Nature by members of the Enabling FAIR Data Steering Committee.

Democratizing data science
MIT researchers are hoping to advance the democratization of data science with a new tool for nonstatisticians that automatically generates models for analyzing raw data.

Getting the most out of atmospheric data analysis
An international team including researchers from Kanazawa University used a new approach to analyze an atmospheric data set spanning 18 years for the investigation of new-particle formation.

Read More: Data News and Data Current Events is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to