Database screening of herbal monomers regulating autophagy by constructing a 'disease-gene-drug' network
| Autor: | Bo Gao, Ming Lu, Xianzhi Meng, Chenjun Hao, Dongbo Xue, Xin Qiao, Zhengpeng Yang, Weihui Zhang |
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| Rok vydání: | 2014 |
| Předmět: |
Programmed cell death
Databases Factual Bioinformatics Gene regulatory network computer.software_genre Neoplasms Drug Discovery Autophagy Medicine Humans Gene Regulatory Networks Human Protein Reference Database Gene Herbal monomer Database Drug discovery business.industry Plant Extracts Gene Expression Profiling Computational Biology General Medicine Genomics Antineoplastic Agents Phytogenic Gene expression profiling Complementary and alternative medicine Gene chip analysis business computer Software Genes Neoplasm Phytotherapy Research Article |
| Zdroj: | BMC Complementary and Alternative Medicine |
| ISSN: | 1472-6882 |
| Popis: | Background Studies suggest an important role of autophagy as a target for cancer therapy. We constructed a "disease-gene-drug" network using the modular approach of bioinformatics and screened herbal monomers demonstrating functions related to autophagy regulation. Methods Based on the microarray results of the gene expression omnibus (GEO) database (GSE2435 and GSE31040, starvation-induced autophagy model), we used the human protein reference database (HPRD) to obtain the protein-protein interaction (PPI) network. In addition, we used the CFinder software to identify several functional modules, performed gene ontology-biological process (GO-BP) functional enrichment analysis using the DAVID software, constructed a herbal monomer-module gene regulatory network using literature search and the Cytoscape software, and then analyzed the relationships between autophagy, genes, and herbal monomers. Results We screened 544 differentially expressed genes related to autophagy, 375 pairs of differentially expressed genes, and 7 gene modules, wherein the functions of module 3 (composed of 7 genes) were enriched in "cell death". Using the constructed herbal monomer-module gene regulatory network, we found that 30 herbal monomers can simultaneously regulate these 7 genes, indicating a potential regulatory role in autophagy. Conclusions Database screening using the disease-gene-drug network can provide new strategies and ideas for the application of herbal medicines in cancer therapy. |
| Databáze: | OpenAIRE |
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