How do I find my gene?
On the home page (https://3dgene.igc.ed.ac.uk) in the search panel select the drop down box, enter your gene name or ID and press submit.
What cell type is available in the 3DGene database?
We currently provide data for GM12878 lymphoblastoid cells.
Why is my gene not available?
We currently only have the 3D structure of active genes in the GM12878 cells.
How do you define a gene?
A gene locus is defined as the genomic region encompassing all its interaction partners.
Why are only three different topologies provided for each gene?
The structure of each gene is simulated 600 times; these are condensed down to the most frequent topologies, and the top three are provided. All structures are available to download from the download page.
Why does each topology have the same contact map?
The contact map is generated by averaging interactions for all 600 gene structures.
How do I change the 3D representation of each gene?
We provide a default space filling model for each gene locus with each bead corresponding to 1000 bp of DNA. To change the representation, select the settings button (spanner) to the right of the 3D visualisation window. Settings are described here (https://molstar.org/viewer-docs/).
What do the different colour beads correspond to?
Some beads can have multiple kinds of mark. In this situation, the bead is coloured according to the order of precedence as listed above (i.e., the top one has the highest order and the bottom one has the lowest order, so a bead with both the K9me3 and active ATAC mark is always coloured as active ATAC).
Can I view structures offline?
Yes, download data from the download page and view in a PDB viewer such as molstar.
Can I take a screen grab of my structure?
Yes, press the shutter icon to the right of the 3D visualisation window.
Will data be available for other cell types?
Yes, we are currently configuring our servers to simulate further cell types. However, each cell type requires approximately 10 million core hours of processing.
What computing platform was used for the simulations?
HiP-HoP simulations were performed on a Linux compute cluster (EDDIE).
Edinburgh Compute and Data Facility web site. 1 December 2021. University of Edinburgh www.ecdf.ed.ac.uk.