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AllegroViva Corporation allegromcode plugin
Allegromcode Plugin, supplied by AllegroViva Corporation, 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/plugin+allegro+mcode/pmc03834854-78-5-10
Average 90 stars, based on 1 article reviews
allegromcode plugin - by Bioz Stars, 2026-09
90/100 stars

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Article Title: Temporal variability and coherence of euphotic zone bacterial communities over a decade in the Southern California Bight
Article Snippet: Modules were identified with the AllegroMCODE plugin using default settings (AllegroViva, Santa Clara, CA, USA).

Article Title: Predicting disease specific spinal motor neurons and glia in sporadic ALS.
Article Snippet: Accepted Manuscript Predicting disease specific spinal motor neurons and glia in sporadic ALS Fabien Dachet, Jiangou Liu, John Ravits, Fei Song PII: S0969-9961(19)30191-3 DOI: https://doi.org/10.1016/j.nbd.2019.104523 Article Number: 104523 Reference: YNBDI 104523 To appear in: Neurobiology of Disease Received date: 17 April 2019 Revised date: 19 June 2019 Accepted date: 1 July 2019 Please cite this article as: F. Dachet, J. Liu, J. Ravits, et al., Predicting disease specific spinal motor neurons and glia in sporadic ALS, Neurobiology of Disease, https://doi.org/ 10.1016/j.nbd.2019.104523 This is a PDF file of an unedited manuscript that has been accepted for publication.. As a service to our customers we are providing this early version of the manuscript.. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form.



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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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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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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