3D Coordination of the genes

[Omar Abduljaleel]

Hi, 

I have a question is there a possible way to measure the distance between genes in the 3d structure? or at least to have the x,y,z coordinates then it would be easy to find the distance?  

Thank you

[lid...@gmail.com]

Hi Omar,

Good question! The browser doesn't provide this feature directly...

I think a doable approach is to find nearest 3D coordinates for the genes you interested, then calculated the distance, usually we use this formula, math.sqrt((x1-x2)**2+(y1-y2)**2+(z1-z2)**2)

[Omar Abduljaleel]

thank you so much but where do you find the 3D coordinates is it in the same site or a different site that provide this information? 

[lid...@gmail.com]

Accidentally just replied to you...

like i replied difference cells might have different models, for example you can start with this https://github.com/lidaof/g3d/blob/master/test/GSM3271347_gm12878_01.impute3.round4.clean.3dg.txt.gz, and then use the coordinates of the genes you interested to check overlapping.

[Omar Abduljaleel]

I have to thank you a lot for providing these numbersDo these values correspond to both hg19 and mm10? and is there a way to recover these values from the model itself so I don't have to bother you alot 😂? 

Thank you,

Omar

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[lid...@gmail.com]

Hi Omar,

The values are just for hg19. There are also models for mouse mm10 from published studies.

if a model is converted to .g3d format, you can use g3dtools to query data out from the file, please see https://github.com/lidaof/g3d/tree/master/g3dtools#query

we found all models from published papers, for example https://pubmed.ncbi.nlm.nih.gov/30166492/