Diving deeper into the gene pool: Innovative software analyzes diseased cells

Diving Deeper Into the Gene Pool: Innovative Software Analyzes Diseased Cells
ScienceDaily (Sep. 28, 2010) — About ten years ago, the discovery of microRNAs -- tiny cellular molecules that regulate our genetic code -- unlocked a world of scientific possibilities, including a deeper understanding of human disease. One new analytical technology is "deep sequencing," which gives scientists the ability to discover invaluable information about human diseases at a genetic level. Now, Tel Aviv University researchers have developed the cutting-edge technology to better analyze these results.

The software, called miRNAkey, was developed by Roy Ronen as part of a team of researchers headed by Dr. Noam Shomron of the Sackler Faculty of Medicine. Dr. Shomron says that miRNAkey searches for microRNA patterns in both healthy and diseased tissues, improving scientists' understanding of the data collected from deep sequencing technology.

The software package was recently described in the journal Bioinformatics.

Making sense of microRNA patterns

Deep sequencing is used to determine the ultimate sequence and expression of cellular DNA or RNA. Once these molecules are extracted, scientists must be able to read the valuable information that the data supplies. Among these are the entire human genome sequence, the expression of the genes from the genome, and the molecules, such as microRNA, which regulate genetic expression. In short, it allows biologists to see further into human genetics and determine where and when genetic malfunctions might occur.

Until now there were very few unified codes that could interpret what information the microRNA held, and none that could run on a local computer or explain ambiguous microRNA behaviors. The solution is the miRNAkey program, says Dr. Shomron. It is designed to identify the relevant microRNA molecule, determine its level, then generate statistically valuable information from it.

"Such identification of microRNAs allows us to manipulate them," Dr. Shomron explains. One example of this potential manipulation is the alteration of malignant tumors. In one study Dr. Shomron and his team of researchers were able to identify the relevant microRNA molecules in an aggressive malignant form of cancer. They then inserted the healthy, non-aggressive form of these microRNAs into the diseased, aggressive molecule. In an animal model, this resulted in a significant slowing of tumor growth.

Results right to the computer screen

With his software, says Dr. Shomron, data obtained from deep sequencing can be quickly and correctly analyzed, allowing scientists to take a deeper look into disease behavior and potentially build specialized treatments with this knowledge. It may also encourage the creation of "smart drugs" which target individual damaged cells.

With a user-friendly interface, miRNAkey can be used on any local computer alongside the proper deep sequencing technology. Unique features such as data statistics and detailed reports provide valuable information about extracted microRNA, notes Dr. Shomron.
Diving deeper into the gene pool: Innovative software analyzes diseased cells

Story Source:
The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by American Friends of Tel Aviv University
[American Friends of Tel Aviv University: Home Page].

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Journal Reference:

1.R. Ronen, I. Gan, S. Modai, A. Sukacheov, G. Dror, E. Halperin, N. Shomron. miRNAkey: a software for microRNA Deep Sequencing analysis. Bioinformatics, 2010; DOI: 10.1093/bioinformatics/btq493