How to map introns to genes

Haky Im

2023-02-22

Categories: FAQ

  • Q: We’ve successfully run the S-PrediXcan and S-MultiXcan methods on our GWAS data using the MASHR sQTL models and have the outputs. My question is, how do I interpret and/or follow up on the results? I see a handful of intron IDs that look significant and I find the relevant single tissue results for those intron IDs.

Find the mapping from intron ids to gene ids in this link https://uchicago.box.com/s/xy71r0su6refrfggivrwc7kpvsxysmmn

  • Q: How should I interpret the z-score? Does a negative z-score for an intron imply that a decrease in the excision of that intron leads to an increase in the GWAS trait? Yes

  • Q: How can I recover the SNPs that are predicted to lead to a decrease in the excision of that intron?

Use this post to query the database file where the prediction weights are included https://predictdb.org/post/2021/07/21/how-do-i-query-the-prediction-model-db/

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Citation

For attribution, please cite this work as

Haky Im (2023). How to map introns to genes. PredictDB. /post/2023/02/22/how-to-map-introns-to-genes/

BibTeX citation

@misc{
  title = "How to map introns to genes",
  author = "Haky Im",
  year = "2023",
  journal = "PredictDB",
  note = "/post/2023/02/22/how-to-map-introns-to-genes/"
}