Minutes instead of months
A tool for automatic RNA analysis has been created
Anatoly Glossev, Vesti
Biologists have developed a BioJupies web application that automatically performs a time-consuming statistical analysis of the "map of working genes" and allows you to exchange this information with colleagues. The whole process takes a few minutes and is almost free. The program was placed in the public domain.
The new application is described in detail in a scientific article published in the journal Cell Systems by a group led by Avi Ma'ayan from Mount Sinai Medical Center in the USA.
As you know, all cells of the human body contain the same DNA molecules. However, cells differ in which genes work in them (are expressed), and which are "silent". It is the pattern of gene expression that distinguishes, say, muscle cells from nerve cells, as well as different types of the latter from each other.
How do I find out which genes work in a particular cell? To do this, it is "enough" to sequence RNA. After all, a gene is, by and large, an instruction for protein synthesis, and its "job" is that this protein is synthesized in the cell. And RNA (more precisely, matrix RNA) is an intermediary in this process, reading information from DNA and transmitting it to the protein synthesizing system.
Gene expression maps have long been an indispensable assistant to researchers in a variety of fields, from evolutionary biology to medicine. However, analyzing such information is not so easy.
The fact is that the genome of even the simplest bacteria encodes more than a thousand proteins. In humans, the number of genes is approaching 30 thousand. This number may not seem so big in comparison with the capabilities of modern computers. But when it comes to complex statistical processing and the search for patterns, it won't take long to sink in such an ocean of information.
Standard RNA sequencing equipment generates "raw", raw output data. Researchers have to deal with their statistical analysis on their own.
Biologists often have to write and test computer programs themselves for this, which takes weeks and months. In addition, such a volume of calculations often cannot be performed on a regular computer. It requires special high-performance equipment to be accessed.
After that, the processed data is processed in the form of an article and sent to a scientific journal. At the same time, from the moment the first version of the text is sent to the publication, it can easily take about a year.
The new application uses cloud computing, so it processes large amounts of data quickly. It provides a whole set of features. Among them there are the most necessary statistical tools for biologists, such as the principal components method, cluster analysis, and so on. The program can also perform tasks specific to biology, for example, it can analyze the representation of functional groups of genes.
The user can analyze their own experimental data or information previously uploaded by someone else.
New data can be uploaded in two formats. The first of them is FASTQ, which has become de facto standard for DNA and RNA sequencing equipment. The second is a table where the rows correspond to genes, and the columns correspond to the studied samples. The table cell shows the expression level of this gene in this sample. Popular formats such as a standard text file, a Microsoft Excel spreadsheet, and so on are supported.
If a scientist wants to use the results of colleagues, he has more than 300 thousand publicly available RNA sequencing datasets at his service. The same methods of statistical analysis can be applied to them.
The newly uploaded data can also be immediately made publicly available. Thus, it is not only a tool for calculating the results, but also a means of making them public.
According to the authors' calculations, the use of BioJupies reduces the cost of data analysis to almost zero (less than one US cent per sample).
"As the amount of biomedical data generated continues to grow exponentially, the tools used for analyzing and sharing them should also be improved," Maayan is sure. "BioJupies not only accelerates data analysis and interpretation, but also provides a completely new way to share results with the global research community."
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