Comprehensive coverage

Kindergartens also have social networks

This communication is the basis for molecular processes called "biological pathways", which take place in the living cell, and are the foundations of the phenomenon of life

"Super-pathways" in the PathCards online database: the map of human biological pathways - each vertex symbolizes a biological pathway, and each connecting line symbolizes a connection between pathways. The colors symbolize the sources from which the routes are taken. Each linked group constitutes a super-pathway, which groups together several closely related pathways, and enables a more efficient study of biological pathways from several different sources. Illustration: Prof. Doron Lantz
"Super-pathways" in the PathCards online database: the map of human biological pathways - each vertex symbolizes a biological pathway, and each connecting line symbolizes a connection between pathways. The colors symbolize the sources from which the routes are taken. Each linked group constitutes a super-pathway, which groups together several closely related pathways, and enables a more efficient study of biological pathways from several different sources. Illustration: Prof. Doron Lantz

Genes also have "social networks": they communicate with other genes, which themselves communicate with other genes. This communication is the basis of molecular processes called "biological pathways", which take place in the living cell, and are the foundations of the phenomenon of life. Therefore, in order to better understand how the human body works, one must learn as much as possible about the biological pathways and the genes that make them up. This is not a simple task: the human genome contains tens of thousands of genes, and each of them communicates with hundreds of other genes. Furthermore, as far as the organization of information is concerned, there has been no uniformity: as in human social networks, which overlap and connect people in different ways, so also the various genetic databases, which provide information on the same biological pathways, are based on standards different for connecting genes, and use different cataloging methods.

Weizmann Institute of Science scientists, led by Prof. Doron Lantz from the Department of Molecular Genetics, have now created a universal database of accessible information on the biological pathways and the genes they contain. The scientists took a uniform mathematical approach, which prevents duplication and makes the most of the information, and through which they combined data collected from a dozen bioinformatic databases into one online database called PathCards. In this global database, data is concentrated on more than 3,000 biological pathways, and they are grouped into approximately 1,000 entities, called "super-pathways". Simplifying and optimizing the accessibility of information in this way will greatly contribute to the advancement of basic and biomedical research.

As recently published in the scientific journal Database (Oxford), the new database provides extensive data on the connectivity of more than ten thousand genes. It does this based on GeneCards - the database of human genes created by Prof. Lantz and his group at the Weizmann Institute of Science almost two decades ago, and has been maintained and nurtured at the institute ever since. The research was led by Dr. Frieda Blinki, who until recently was a post-doctoral researcher in the laboratory, and was attended by Noam Nativ, Dr. Gil Shtelzer, Shahar Zimmerman, Dr. Tzipi Ini Stein, as well as Merlin Shafran, the head of the GeneCards team.
Since the PathCards database unites many biological pathways under one roof, it actually presents the entire genome as a complex fabric of small "social networks". Using these networks, scientists can now find a common denominator between genes that previously were not known to be related, if only by virtue of their belonging to the same new and unified super-pathway. This is similar to a situation where strangers are connected through a mutual friend who belongs to two different social networks.

The PathCards database allows scientists to perform a quick in-depth search of all human superpathways. For example, a search by the insulin gene - the hormone that controls the metabolism of sugar in the body - brings up a list of more than 160 super-pathways. But a scientist looking for a connection between insulin and, for example, adrenaline, will immediately find a subset of six super-pathways, linking insulin and the adrenaline receptor, thus revealing the points of connection between the two hormones, and their details.

Indeed, one of the main goals of this research project is to help scientists identify unexpected and important relationships between different genes, in order to discover additional genes related to the formation of different diseases, and to develop new drugs. Using PathCards it is possible to locate "incriminating information": if gene A, which is in a certain super-pathway, is already known to cause a disease, and gene B is also found in the same super-pathway, it can be concluded that the latter may also be related to this disease. Prof. Lantz and members of his group even developed another bioinformatics tool, called VarElect, which is used to analyze DNA sequencing data in the genomes of sick people: while cross-referencing data with GeneCards and PathCards, the tool enables the identification of the specific gene that causes the disease.

One response

  1. Interesting and very bad article, because it does not explain its main terms. What is a biological pathway? How does a garden communicate with a garden?

Leave a Reply

Email will not be published. Required fields are marked *

This site uses Akismat to prevent spam messages. Click here to learn how your response data is processed.