Joint multi-omics dimensionality reduction approaches for CAKUT data using peptidome and proteome data
Brief description In (Cantini et al. 2020), Cantini et al. evaluated 9 representative joint dimensionality reduction (jDR) methods for multi-omics integration and analysis and . The methods are Regularized Generalized Canonical Correlation Analysis (RGCCA), Multiple co-inertia analysis (MCIA), Multi-Omics Factor Analysis (MOFA), Multi-Study Factor Analysis (MSFA), iCluster, Integrative NMF ...
Type: Snakemake
Creators: Ozan Ozisik, Juma Bayjan, Cenna Doornbos, Friederike Ehrhart, Matthias Haimel, Laura Rodriguez-Navas, José Mª Fernández, Eleni Mina, Daniël Wijnbergen
Submitter: Juma Bayjan
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 ...
Type: Snakemake
Creators: Woosub Shin, Friederike Ehrhart, Juma Bayjan, Cenna Doornbos, Ozan Ozisik
Submitter: Juma Bayjan
Common Workflow Language example that illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI). This workflow returns a resulting protein structure and simulated 3D trajectories.