Database for Hedgehog Signal Pathway Research Created
October 20, 2005 8:47 PM
SF State’s biology and computer science departments have worked together to create one of the most popular Internet databases for the highly researched Hedgehog Signal Pathway.
Hedgehog is the nickname of a secreted protein found in numerous organisms, including humans. When the Hedgehog is received, it activates a series of events in the cell, which is referred to as a signal pathway. These events can lead to mutations that result in different types of cancer, according to cell and molecular Biology Professor Felipe-Andres Ramirez-Weber.
One of the reasons the Hedgehog Signal Pathway is widely studied is because of the importance of the protein and its involvement in different types of diseases, according to Ramirez-Weber. The Hedgehog protein has been linked to various types of cancer including prostate, breast and pancreatic cancer.
“A cell (after receiving the protein Hh) will make important decisions, like to divide or turn on a typical protein that can make a hair, or make a nerve,” explained Ramirez-Weber, who does research on different signal pathways. “Because there are so many different components in interpreting the reception of Hedgehog, there are many diseases associated with it.”
The Ramirez-Weber Lab, an SF State biology lab located in Hensill Hall, gathers and does research to create a free and easy-to-use database which covers all aspects of the Hedgehog Signal Pathway, also referred to as Hh by researchers.
The database was created because the Hedgehog pathway has no central database for people researching the Hh protein, according to Ramirez-Weber, who discovered cytonemes(projections that different proteins expell that enable the proteins to morph cells, like Hh).
“This information (Hh research) is available, but we collect it all and put it in an easily accessible and organized format,” said Ramirez-Weber. “In a matter of clicks you can get the gene structure, the structure of the protein, and the information the researchers needs.”
Students working in the Ramirez-Web Lab validate by hand which gene sequences are valid, conduct and sort through research, and update the Web site regularly according to Kieran Hervold, 26-year-old biology senior who designs the Hedgehog Web site.
The Ramirez-Weber Lab conducts its own research on different strains of fruit flies in order to track the differences in genetics. It then uses these differences and compares it with the Hh protein, according to Ramirez-Weber.
“I try to figure the modes of transport of the wingless gene,” said 29-year-old Ouma Onguka, who is a graduate student in cellular and molecular biology and researches the genetics of wingless fruit flies in the lab. “The modes of transport in the wingless gene are similar to those of the Hedgehog.”
As the months go by, the online database’s popularity continues to grow. It is now ranked number one in its Google search class. In August the site received 5,000 hits and since then it has had more than 15,000 hits a month.
The two departments are in their final stages of making the database interactive for Hh research by adding an annotizer -an interactive tool that can be used by people viewing the website.
“We’re adding an innovated functionality that isn’t easy to find anywhere else,” said Professor Dragutin Petkovic, Computer Science Chair.
According to Petkovic, the database is currently in its first phase and phase two will enable its users to leave comments and post new findings on the different research called collaboration technology.
“The beauty of this Web site is the quality of the data,” said Petkovic.
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