issues in eMAGMA GENE-SET ANALYSIS

[changxuling]

Hi,

I am trying to run through the tutorial using Amygdala_emagma.genes.raw inside Amygdala_outputs.zip but encountered the attached issue. Could you please kindly help with that?

Also the eMAGMA Co-expression network files is currently only avaiable for brain tissues. May I know whether it is available for other tissues? if not, could you please kindly share the codes that you have used for the brain tissues?

The last question will be I notice in the paper that the data is from EUR. How does this work for other ethnicity groups?

Thank you.

Cheers
Shirley

[gerringz]

Hi Shirley,
Happy to share the co-expression files, will organise the transfer. We have generated annotation files for brain tissues and whole blood, however these are only available for EUR ancestry defined in GTEx. I can assist with generation of ancestry-specific annotation files if you have in-house data.
Regards,
Zac

[jw9507]

Hi Zac,

We have same problem on generation of annotation files for the tissues of interest, because we do not know the detailed process of the generation. Could you help us to generate a European annotation files for retina which could be obtained from EyeGEx QTL dataset. The dataset can access from GEO with ID GSE115828 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE115828).

Additionally, we are also trying to add the expression data for retina to the general gene expression data for 54 tissues from GTEx v8 (https://fuma.ctglab.nl/tutorial/download_variants), so that we can perform gene property analysis for retinal tissue specificity.
gtex_v8_ts_avg_log2TPM.zip

The combination of the differential expression for retina and GTEx v8 specific expression differentially expressed genes (https://fuma.ctglab.nl/tutorial/download_variants) is also greatly useful.
gtex_v8_ts_DEG.txt

These are important and useful for our research in Ophthalmology. We greatly appreciated your help! We would be very grateful if we could receive an email from you with a positive reply.

Regards,
Jiawei Chen
jiawei_chen20@foxmail.com

Hi Shirley, Happy to share the co-expression files, will organise the transfer. We have generated annotation files for brain tissues and whole blood, however these are only available for EUR ancestry defined in GTEx. I can assist with generation of ancestry-specific annotation files if you have in-house data. Regards, Zac