GREG -The Gene Regulation Graph Database

Hello everyone,
I am a bioinformatician at Guangzhou Medical University in China. My group has developed a new graph database to study gene regulation using Neo4j and we would like to let you know.

Our paper: GREG—studying transcriptional regulation using integrative graph databases | Database | Oxford Academic
Our website:

We are relatively new to Neo4j so any comments are welcome.


Welcome antoniocrmora.
Interesting project and graph. I noticed that the relationships are not directed in your graph visualization, is that an intentional modeling decision? I usually think of all relationships as directional, left, right or both.

I'm interesting in your thoughts on this aspect, in general and in terms of how you modeled this data.

Hi Joel,

Most of the interactions in GREG come from high-throughput technologies that can't offer directionality information by design (I think this is better represented by an undirected edge than by a double-arrow, and that is the way is treated in the biological literature). Biochemical directional information (arrows) usually design chains of reactions (so-called "pathways") and, in some cases, you may need the double-arrow to design pathways that go both ways. Such information is stored in a different type of databases, coming from different types of technologies (or predicted by algorithms).

If we decided to mix the two types of information in our database (interactions and pathways, undirected and directed), which we didn't, we may need to distinguish between directed, double-arrow, and undirected edges; and we may need the ability to have one undirected and one directed relationship between the same two nodes. An alternative would be to add pathway/direction information as properties, so the user could see that in some cases there is available information about direction, while in most cases not. That is just what I think now, but we haven't tried any of this yet.

Thanks for your comment.

Hi Antonio,