Gene Regulatory Network Graphs?
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12.5 years ago

What databases are available for gene regulatory network graphs starting from a given gene? For example, starting from p53 gene, where can I find a gene regulatory network image that can be exported or embedded to another website?

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Can you clarify your use of the term "graph"? Do you mean the usual network graph, with nodes & edges (a visual representation of an algorithm, with the edges having some mathematical meaning), or do you just mean a figure (a visual representation of someone's artistic conception of biol data)? There are many of the latter, not many that will give you the former.

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12.5 years ago

There are many ways and resources to do what you want. If you only want a nice image, I think that the best is to use the one from Biocarta (http://www.biocarta.com/pathfiles/h_p53Pathway.asp):

enter image description here

Please remember to provide a link back to Biocarta in the page. Also, I am not sure that biocarta allows embedding of its images on other websites, so please check that.

Other resources for pathway annotation are Reactome, Wikipathways and Kegg (click on the link to go to the p53 page there), so you may want to check them.

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12.5 years ago

AFAIK there are not many sites that will do what you want, ready made for export or linkage to another site. And whatever you want, you want it to be well curated. Beware of the poorly-curated, or context-independent network graph. One site is the Pathway Interaction Database at NCI. If you are lucky, your gene regulatory network will be in their data set. If it's not, it's not, and you may have to either 1) get the image from a high-quality publication where the data are good & true about the network members or 2) draw it yourself using something like BioTapestry deriving it from multiple publications that validate one another.

Searching the PID for "p53" shows that for that one (not surprisingly) you may be in luck.

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