COLONOMICS - predictive models for normal colon gene expression and DNA methylation for TWAS and MWAS
DOI10.5281/zenodo.6334768Zenodo6334768MaRDI QIDQ6702957FDOQ6702957
Dataset published at Zenodo repository.
Anna Diaz-Villanueva, Victor Moreno, Virginia Diez-Obrero, Rebeca Sanz-Pamplona
Publication date: 7 March 2022
Copyright license: Creative Commons Attribution 4.0 International
We providesignificant SNP prediction models derived from the COLONOMICS data (https://www.colonomics.org). Genotypes were obtained by Affymetrix 6.0 array, imputed to TopMed panel. Gene expression was obtained from Affymetrix U219 array, DNA methylation was obtained with Illuminan 450K array and miRNA expression was obtained by NGS.We provide SNP prediction models for 1,758 genes, 30,530 CpG probes and 38 miRNAs obtained from colon normal biopsy samples. These features can be predicted from SNPs located within 1Mb, which we assumed they act through cis mechanisms. We includethe models summary statistics and corresponding SNP weights in SQLite objects. Models were trained using the elastic net procedure employed in the PredictDB pipeline (https://predictdb.org), according to which only models with a predictive performance p-value 0.05 and R2 0.1 are considered significant. We adjusted the models by basic covariates, i.e., sex, age, tissue type and colon anatomic location where biopsies were collected (left and right colon). Genome coordinates refer to GRCh37/hg19.
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