Corpus overview


Overview

MeSH Disease

Human Phenotype

Transmission

There are no transmission terms in the subcorpus


Seroprevalence

There are no seroprevalence terms in the subcorpus

    displaying 1 - 1 records in total 1
    records per page




    Finding disease modules for cancer MESHD and COVID-19 in gene co-expression networks with the Core&Peel method

    Authors: Marta Lucchetta; Marco Pellegrini

    doi:10.1101/2020.05.27.118414 Date: 2020-05-27 Source: bioRxiv

    Diseases imply dysregulation of cells functions at several levels. The study of differentially expressed genes in case-control cohorts of patients is often the first step in understanding the details of the cells dysregulation. A further level of analysis is introduced by noticing that genes are organized in functional modules (often called pathways), thus their action and their dysregulation may be better understood by the identification of the modules most affected by the disease ( aka disease MESHD modules, or active subnetworks). We describe how an algorithm based on the Core&Peel method developed originally for detecting protein complexes in PPI networks, can be adapted to detect disease modules in co-expression networks of genes. We first validate Core&Peel for the easier general task of functional module detection by comparison with 42 methods participating in the Disease Module Identification DREAM challenge of 2019. Next, we use four specific disease test cases ( colorectal cancer MESHD cancer, prostate HP prostate cancer MESHD, asthma HP asthma MESHD and rheumatoid arthritis HP rheumatoid arthritis MESHD), four state-of-the-art algorithms (ModuleDiscoverer, Degas, KeyPathwayMiner and ClustEx), and several pathway databases to validate the proposed algorithm. Core&Peel is the only method able to find significant associations of the predicted disease module with known validated relevant pathways for all four diseases. Moreover for the two cancer MESHD data sets, Core&Peel detects further nine relevant pathways enriched in the predicted disease module, not discovered by the other methods used in the comparative analysis. Finally we apply Core&Peel, along with other methods, to explore the transcriptional response of human cells to SARS-CoV-2 infection MESHD, at a modular level, aiming at finding supporting evidence for drug repositioning efforts.

The ZB MED preprint Viewer preVIEW includes all COVID-19 related preprints from medRxiv and bioRxiv, from ChemRxiv, from ResearchSquare, from arXiv and from Preprints.org and is updated on a daily basis (7am CET/CEST).
The web page can also be accessed via API.

Sources


Annotations

All
None
MeSH Disease
Human Phenotype
Transmission
Seroprevalence


Export subcorpus as...

This service is developed in the project nfdi4health task force covid-19 which is a part of nfdi4health.

nfdi4health is one of the funded consortia of the National Research Data Infrastructure programme of the DFG.