EJP-RD WP13 case-study: CAKUT proteome, peptidome and miRNome data analysis using WikiPathways
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Workflow Type: Snakemake

In this analysis, we created an extended pathway, using the WikiPathways repository (Version 20210110) and the three -omics datasets. For this, each of the three -omics datasets was first analyzed to identify differentially expressed elements, and pathways associated with the significant miRNA-protein links were detected. A miRNA-protein link is deemed significant, and may possibly be implying causality, if both a miRNA and its target are significantly differentially expressed.

The peptidome and the proteome datasets were quantile normalized and log2 transformed (Pan and Zhang 2018; Zhao, Wong, and Goh 2020). Before transformation, peptide IDs were mapped to protein IDs, using the information provided by the data uploaders, and were summarized into single protein-level values using geometric mean. The miRNome dataset was already normalized and transformed; thus, the information of their targeting genes was simply added to each miRNA ID, using the information provided by miTaRBase (Huang et al. 2019). As a result, all three datasets had been mapped to their appropriate gene product-level (or, protein-level) identifiers.

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Version 1 (earliest) Created 20th Apr 2022 at 17:59 by Juma Bayjan

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Created: 20th Apr 2022 at 17:59

Last updated: 27th Oct 2022 at 16:16

Last used: 7th Dec 2022 at 00:16

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