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Modular Analysis of Bioinformatics Demonstrates a Critical Role for NF-κB in Macrophage Activation

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Abstract

To achieve the goal of identifying the gene groups that regulated macrophage activation, a total of 925 differentially expressed genes of activated macrophages were found at the intersection of the three series (GSE5099-1, GSE5099-2, and GSE18686) from the Gene Expression Omnibus (GEO) database, and a sub-network was constructed based on the protein-protein interaction (PPI) network. Four communities (K = 3) were identified from the sub-network using the CFinder software. Community 1 was considered as the gene group of interest base on the heat map. GO-BP and KEGG enrichment analysis with the DAVID software showed that the functions of the 14 genes in community 1 were mainly related to the NF-κB pathway. A network was constructed using the Cytoscape software. The diagram showed that STAT1, NFKBIA, NFKAIB, JUN, and RELA were the key genes in the regulation of macrophage activation. Among these genes, RELA (NF-κB P65) was an important member of the NF-κB family, while NFKBIA (IκBα) and NFKAIB (IκBβ) were the inhibitory factors of NF-κB. Small molecules capable of regulating these five genes were identified via the CMap software, and a network diagram was generated using the Cytoscape software to provide a reference for the development of new drugs that regulate macrophage activation.

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ACKNOWLEDGEMENTS

This study was supported by the National Natural Science Foundation of China (81370566).

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Authors and Affiliations

  1. Central Laboratory, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, People’s Republic of China

    Yingmei Zhang

  2. Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, People’s Republic of China

    Yingmei Wang, Bei Sun, Weihui Zhang & Dongbo Xue

  3. Department of Surgery, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90064, USA

    Ming Lu & Xin Qiao

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  1. Yingmei Zhang
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Correspondence to Dongbo Xue.

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Zhang, Y., Wang, Y., Lu, M. et al. Modular Analysis of Bioinformatics Demonstrates a Critical Role for NF-κB in Macrophage Activation. Inflammation 37, 1240–1253 (2014). https://doi.org/10.1007/s10753-014-9851-z

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