Protein Interaction Network Analysis

A database called Search Tool for the Retrieval of Interacting Genes (STRING) is used to study the functional protein association networks (Szklarczyk et al., 2017 (link)). The filtered DEGs had already been added to the STRING database. All PPI pairs with a cumulative score greater than 0.4 were retrieved. High-degree nodes seem to be essential for maintaining the network’s overall stability. The degree of all nodes was calculated by Cytoscape (v3.6.1) plugin cytoHubba using the MCC algorithm (Chin et al., 2014 (link)), in this experiment, the genes with the top 10 highest MCC score values were considered as hub genes.

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Guo J., Feng S., Yu H., Ou B., Jiang D., Zhuang W., Ding C., Chen X., Zhang M., Ling Y., Zeng Y, & Qiu H. (2023). Transcriptomic study of gastrointestinal stromal tumors with liver metastasis. Frontiers in Genetics, 14, 1007135.

Publication 2023

Chin Genes Mcc genes Protein

Corresponding Organization :

Other organizations : Xiamen University

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Variable analysis

independent variables

None explicitly mentioned

dependent variables

Degree of all nodes calculated by Cytoscape (v3.6.1) plugin cytoHubba using the MCC algorithm
Genes with the top 10 highest MCC score values considered as hub genes

control variables

None explicitly mentioned

controls

No positive or negative controls specified by the authors

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