The notch signaling pathway is one of many routes through which cells communicate with each other.
In mammalian embryos, such pathways are used to send information from cell to cell about the “formation of teeth and hair and almost anything else you can imagine in the organism,” said Dr. Karen Artzt, Ashbel Smith Professor in the Section of Molecular Genetics, Microbiology and Immunology. And, components of the pathways have shown to be important in cancer.
This is a detail of the map of the mouse notch signaling pathway. The map, a graphic database, shows the relationships between components of the pathway. Click on the detail to go the full map.
The pathway is better understood in organisms like the fruit fly (drosophila) and worm (c. elegans) used in research.
Artzt’s lab genetically engineers mice carrying germline mutations in this pathway in order to elucidate the mechanisms of cell commitment in the early mammalian embryo. For mammals in general, this type of manipulation is more complicated than in flies or worms due to longer gestation periods.
A graphical database showing the pathway and the relationships between the nodes on the pathway would be valuable for students learning to find their way around the pathway as well as to experienced researchers.
And that’s what a Ph.D. student in Artzt’s lab and an undergraduate student studying computer science and neurobiology have put together. It’s
at http://web.biosci.utexas.edu/artzt_lab/notch/. It is available
to users at UT Austin.
Users can find step-by-step instructions on how to navigate the database by simply clicking on the two help buttons designated by question marks.
Julius Barsi, a Ph.D. student in the lab of Dr. Karen Artzt, provided the information for the database and keeps it up to date.
The graphical interface is meant to represent two adjacent cells. This model displays component names, type, whether it’s a gene or a protein and their position within the pathway. All components are “clickable” so as to reveal more information about itself and what it’s related to.
“This really all came about that I was writing up our paper and I needed to have all the information of this complicated molecular cascade at my fingertips,” Julius Barsi, the Ph.D. student, said. “I just couldn’t remember all the components.”
Artzt said it’s not just students who need such a database. “It’s just a terribly complicated cell signaling pathway.”
Barsi gathered the information for the database. Zack Mahdavi,
a senior studying computer science and neurobiology, did the programming.
He had an Undergraduate Research Fellowship from the university
to pursue the project.
Barsi had three things in mind when they sat down to put it together:
A cross-reference search engine in which the user could query a mammalian gene and it would search across databases and find scientific papers in relation to the pathway.
The search brings up not just the paper, but it goes directly to the experiment supporting its position within the pathway.
Zack Mahdavi, a senior in computer science and neurobiology, programmed the database.
“You can judge for yourself the nature and quality of the data and see if you believe it or not,” Barsi said. “Because in many cases you can have an experiment and it can be subject to interpretation. It was really neat to compile all that together.”
UT Austin users get access to the papers through licenses the university has with the journals.
The graphical interface, which makes it easier to navigate around the pathway.
Barsi picked up the idea at a conference in Germany, where another lab made a presentation with a graphical interpretation analogous to that used for computer chips, but for molecular biology. They have a whole annotation system that is tailored for biology specifically and you can make a blueprint of what you believe is going on.
Barsi will update the database as new information is published in journals.
