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mcode plugin  (Cytos Inc)

 
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    Structured Review

    Cytos Inc mcode plugin
    Mcode Plugin, supplied by Cytos Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/mcode+plugin/mcode+plugin/pm37986009-96-14-4
    Average 90 stars, based on 1 article reviews
    mcode plugin - by Bioz Stars, 2026-09
    90/100 stars

    Images

    Related Articles

    Functional Assay:

    Article Title: Molecular characteristics associated with ferroptosis in hepatocellular carcinoma progression.
    Article Snippet: The aim of this study was to investigate the genes associated with ferroptosis and the progression of hepatocellular carcinoma (HCC).. The RNA sequencing data of erastin-induced ferroptosis in HCC cells were downloaded from the Sequence Read Archive database with accession number SRP119173.. The microarray dataset GSE89377 of HCC progression was downloaded from the Gene Expression Omnibus database.

    Protein-Protein interactions:

    Article Title: Molecular characteristics associated with ferroptosis in hepatocellular carcinoma progression.
    Article Snippet: The aim of this study was to investigate the genes associated with ferroptosis and the progression of hepatocellular carcinoma (HCC).. The RNA sequencing data of erastin-induced ferroptosis in HCC cells were downloaded from the Sequence Read Archive database with accession number SRP119173.. The microarray dataset GSE89377 of HCC progression was downloaded from the Gene Expression Omnibus database.

    other:

    Article Title: Identifying individualized prognostic signature and unraveling the molecular mechanism of recurrence in early-onset colorectal cancer.
    Article Snippet: The Cytoscape software (https:// cytos cape. org/) was used to visualize the network, and MCODE (Molecular complex detection) plugin was applied to cluster the PPI network based on topology and find densely connected regions.



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    Identification of gene modules related to pyroptosis via comprehensive analysis of PPI network and WGCNA. A PPI network was constructed using the STRING database. B PPI network was visualized using Cytoscape software and the relevance level were ranked in different colors. C Twenty-one hub genes and their connections were identified via the <t>MCODE</t> algorithm. D Determination of WGCNA soft threshold. E Gene clustering tree (dendrogram) was obtained by hierarchical clustering of adjacency-based dissimilarity. F The correlation heatmap of gene modules and phenotypes. G The venn diagram showed the genes shared by PPI hub genes and the WGCNA magenta module
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    Image Search Results


    Identification of gene modules related to pyroptosis via comprehensive analysis of PPI network and WGCNA. A PPI network was constructed using the STRING database. B PPI network was visualized using Cytoscape software and the relevance level were ranked in different colors. C Twenty-one hub genes and their connections were identified via the MCODE algorithm. D Determination of WGCNA soft threshold. E Gene clustering tree (dendrogram) was obtained by hierarchical clustering of adjacency-based dissimilarity. F The correlation heatmap of gene modules and phenotypes. G The venn diagram showed the genes shared by PPI hub genes and the WGCNA magenta module

    Journal: Journal of Translational Medicine

    Article Title: Transcriptome profile and immune infiltrated landscape revealed a novel role of γδT cells in mediating pyroptosis in celiac disease

    doi: 10.1186/s12967-023-04359-1

    Figure Lengend Snippet: Identification of gene modules related to pyroptosis via comprehensive analysis of PPI network and WGCNA. A PPI network was constructed using the STRING database. B PPI network was visualized using Cytoscape software and the relevance level were ranked in different colors. C Twenty-one hub genes and their connections were identified via the MCODE algorithm. D Determination of WGCNA soft threshold. E Gene clustering tree (dendrogram) was obtained by hierarchical clustering of adjacency-based dissimilarity. F The correlation heatmap of gene modules and phenotypes. G The venn diagram showed the genes shared by PPI hub genes and the WGCNA magenta module

    Article Snippet: Furthermore, we used the MCODE plugin app ( https://sourceforge.net/projects/mcode/ ) within Cytoscape to identify hub genes and calculate the degrees of interaction between DEGs to visualize the ranking.

    Techniques: Construct, Software