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### Gene expression data and preprocessing {#sec:data_gtex} | ||
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We downloaded GTEx v8 data for all tissues, normalized using TPM (transcripts per million), and focused our primary analysis on whole blood, which has a good sample size (755). | ||
We selected the top 5,000 genes from whole blood with the largest variance after standardizing with $log(x + 1)$ to avoid a bias towards highly-expressed genes. | ||
We then computed Pearson, Spearman, MIC and CCC on these 5,000 genes across all 755 samples on the TPM-normalized data, generating a pairwise similarity matrix of size 5,000 x 5,000. | ||
We downloaded gene expression data from GTEx v8 ([https://gtexportal.org/](https://gtexportal.org/)) for all tissues, normalized using TPM (transcripts per million), and focused our primary analysis on whole blood, which has a good sample size (755). | ||
We selected the top 5,000 genes from whole blood with the largest variance after standardizing with $log(x + 1)$ to avoid a bias toward highly expressed genes. | ||
We then computed Pearson, Spearman, MIC and CCC on these 5,000 genes across all 755 samples, generating a pairwise similarity matrix of size 5,000 x 5,000. |