title: Database screening of herbal monomers regulating autophagy by constructing a "disease-gene-drug" network.
abstract: 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.
authors.forename: Chenjun
authors.initials: C
authors.lastname: Hao
authors.forename: Zhengpeng
authors.initials: Z
authors.lastname: Yang
authors.forename: Bo
authors.initials: B
authors.lastname: Gao
authors.forename: Ming
authors.initials: M
authors.lastname: Lu
authors.forename: Xianzhi
authors.initials: X
authors.lastname: Meng
authors.forename: Xin
authors.initials: X
authors.lastname: Qiao
authors.affiliation: Department of General Surgery, the First Affiliated Hospital of Harbin Medical University, Harbin, China. Dongbo_xue@126.com.
authors.forename: Dongbo
authors.initials: D
authors.lastname: Xue
authors.forename: Weihui
authors.initials: W
authors.lastname: Zhang
mesh_terms: D000972:Antineoplastic Agents, Phytogenic / Q000494:pharmacology* / Q000627:therapeutic use; D001343:Autophagy / Q000187:drug effects* / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D016208:Databases, Factual; D055808:Drug Discovery / Q000379:methods*; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D052138:Genes, Neoplasm; D006801:Humans; D009369:Neoplasms / Q000188:drug therapy / Q000235:genetics*; D008517:Phytotherapy; D010936:Plant Extracts / Q000494:pharmacology* / Q000627:therapeutic use; D012984:Software
chemical_list: D000972:Antineoplastic Agents, Phytogenic; D010936:Plant Extracts