Jan 27, 2025

Public workspaceUnveiling Hub Genes and Biological Pathways: A Bioinformatics Analysis of Trauma-Induced Coagulopathy (TIC)

DOI
dx.doi.org/10.17504/protocols.io.4r3l29bz4v1y/v1
  • 1Yuncheng Central Hospital affiliated to Shanxi Medical University;
  • 2Shanxi Academy of Medical Sciences,Tongji Shanxi Hospital;
  • 3Hebei province Xingtai Third People's Hospital
lin gang zhang
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DOI: dx.doi.org/10.17504/protocols.io.4r3l29bz4v1y/v1
Protocol Citation: lin gang zhang, Bo Li, Jing Liu, Yanfeng Bian, Ying Zhou, Ying Zhou 2025. Unveiling Hub Genes and Biological Pathways: A Bioinformatics Analysis of Trauma-Induced Coagulopathy (TIC). protocols.io https://dx.doi.org/10.17504/protocols.io.4r3l29bz4v1y/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: January 25, 2025
Last Modified: January 27, 2025
Protocol Integer ID: 119067
Keywords: Biological Markers, Traumatic Coagulopathy, Bioinformatics, Differentially Expressed Genes, Pathway Analysis, Protein-Protein Interaction Network, Hub Genes, ROC Analysis.
Funders Acknowledgements:
2023 Yuncheng City Basic Research Program (Free Exploration Category) Projects
Grant ID: YCKJ-2023052
Disclaimer
This protocol is under a Creative Commons license. Please credit the author(s) when using this protocol in your work.
Abstract
This protocol outlines a bioinformatics approach to identify hub genes and associated pathways in Trauma-Induced Coagulopathy (TIC) using microarray datasets from the GEO database. The methodology includes the identification of differentially expressed genes (DEGs), pathway analysis, and the construction of a Protein-Protein Interaction (PPI) network. The expected results include the identification of key genes and pathways associated with TIC, which could lead to novel biomarkers for its diagnosis and therapeutic targets.
Materials
Materials Required
Microarray Dataset: Dataset Name: GSE223245 Source: Gene Expression Omnibus (GEO) Database Description: This dataset includes gene expression data used for the identification of differentially expressed genes (DEGs) associated with trauma-induced coagulopathy (TIC). Software and Tools: R (v4.0 or higher): For statistical analysis and DEG identification. Bioconductor packages: Used for data preprocessing and DEG analysis (e.g., limma,edgeR). Cytoscape (v3.8.2 or higher): For constructing the Protein-Protein Interaction (PPI) network. CytoHubba plugin: To identify hub genes in the PPI network. MCODE plugin: For module detection in the PPI network. CTD (Comparative Toxicogenomics Database): Used for further analysis of gene-disease associations. Web Tools: DAVID (Database for Annotation, Visualization, and Integrated Discovery): For GO and KEGG pathway enrichment analysis. ROC Analysis Software: R (v4.0 or higher): For conducting Receiver Operating Characteristic (ROC) curve analysis to evaluate the diagnostic potential of hub genes.
Data Acquisition
Objective: Obtain microarray datasets for analysis. Action: Download the dataset GSE223245 from the Gene Expression Omnibus (GEO) database.
Identification of Differentially Expressed Genes (DEGs)
Objective: Identify the DEGs from the dataset. Action: Process the dataset to extract upregulated and downregulated genes.
Functional Enrichment Analysis (GO and KEGG)
Objective: Perform gene functional enrichment analysis. Action: Conduct Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses on the DEGs.
Construction of Gene-Concept Network
Objective: Establish a relationship between the genes and their functions. Action: Construct a gene-concept network to visualize gene interactions and functions.
Construction of Protein-Protein Interaction (PPI) Network
Objective: Build a PPI network for further analysis. Action: Use CytoHubba, MCODE, and CTD scores to identify hub genes linked to trauma-induced coagulopathy (TIC).
Identification of Hub Genes
Objective: Identify significant hub genes related to TIC. Action: Analyze the PPI network to pinpoint crucial hub genes.
ROC Analysis of Hub Genes
Objective: Evaluate the diagnostic potential of the hub genes. Action: Perform Receiver Operating Characteristic (ROC) analysis on the hub genes to assess their clinical relevance.
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