Mapping between regions and genes

[fvalle1]

Hello,

in the 08-calculate_gen_pvals.ipynb notebook there is a step to Load the transcriptomic expression of each brain gene, the geodesic distance matrix of each region from Desikan-Killiany atlas and the pseudo R2 maps, such a step loads these files: gen_exp_in_LH_SP70.csv desikan_LH_geo_dist.csv mdmr_rsquare_euclidean_desikan_LH.csv.

May I ask you where did you get those files or how did you generate them? Or, more generally, how do you map your regions IDs to gene names?

Thank you!

[ajimenezmarin]

Hello,

• The file gen_exp_in_LH_SP70.csv is the one containing the transcriptomic profiles, and it has been obtained using our own code following the paper. But now, there exist a tool for doing the same more easily and reproducible, so I recommend you to use this tool.
• The file desikan_LH_geo_dist.csv contain the geodesic distances between the ROIs of the parcellation we are using, and has been obtained using the tool brainSMASH. The distance between subcortical and cortical ROIs has been performed using the euclidean distance.
• The file mdmr_rsquare_euclidean_desikan_LH.csv can be obtained using the notebook 05-mdmr_subtypes_vs_TDC.ipynb.

I hope I answered all your questions, but if you need something else, please tell us!