Xue Yang1,2,3, Qi-Ni Cheng1,2,3, Jiang-Feng Wu1,2,3,4, Wen-Bing Ai3,5, Lan Ma1,3. 1. Medical College, China Three Gorges University Yichang, China. 2. Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University Yichang, China. 3. Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University Yichang, China. 4. Department of Organ Fibrosis and Targeted Drug Delivery, The First People's Hospital of Yichang Yichang, Hubei, China. 5. The Yiling Hospital of Yichang Yichang, China.
Abstract
OBJECTIVE: To analyze differentially expressed genes (DEGs) related to liver fibrosis, and clarify the key genes and the possible targets in the progression of liver fibrosis. METHODS: Using microarray datasets, GSE38199 was extracted from Gene Expression Omnibus (GEO), and a bioinformatics method was performed to find DEGs and transcription factors related to liver fibrosis. RESULTS: A total of 58 DEGs were screened out according to GEO2R online analysis tool, which included 49 up-regulated and 9 down-regulated genes. These DEGs were mainly involved in formation with the extracellular region and extracellular exosome through gene ontology (GO) enrichment analysis. Kyoto Encyclopedia of Gene and Genome (KEGG) pathway enrichment analysis showed that DEGs mainly participated in the PI3K-Akt signaling pathway, focal adhesion, ECM-receptor interaction, and metabolic pathways. Based on the results of the Protein-Protein Interaction (PPI) network and Molecular Complex Detection (MCODE) analysis, 9 key genes (COL1A1, FBN1, BGN, COL6A3, MMP2, FBLN5, LUM, PDGFRB, LOXL1) were screened out. A total of 30 transcription factors were found according to these 9 key genes, of which 4 transcription factors (Stat3, Trp53, NF-κB1, Sp1) were enriched. CONCLUSION: Stat3, Trp53, NF-κB1, and Sp1 were all related to the development of liver fibrosis, and FBLN5 might be a target for liver fibrosis. IJCEP
OBJECTIVE: To analyze differentially expressed genes (DEGs) related to liver fibrosis, and clarify the key genes and the possible targets in the progression of liver fibrosis. METHODS: Using microarray datasets, GSE38199 was extracted from Gene Expression Omnibus (GEO), and a bioinformatics method was performed to find DEGs and transcription factors related to liver fibrosis. RESULTS: A total of 58 DEGs were screened out according to GEO2R online analysis tool, which included 49 up-regulated and 9 down-regulated genes. These DEGs were mainly involved in formation with the extracellular region and extracellular exosome through gene ontology (GO) enrichment analysis. Kyoto Encyclopedia of Gene and Genome (KEGG) pathway enrichment analysis showed that DEGs mainly participated in the PI3K-Akt signaling pathway, focal adhesion, ECM-receptor interaction, and metabolic pathways. Based on the results of the Protein-Protein Interaction (PPI) network and Molecular Complex Detection (MCODE) analysis, 9 key genes (COL1A1, FBN1, BGN, COL6A3, MMP2, FBLN5, LUM, PDGFRB, LOXL1) were screened out. A total of 30 transcription factors were found according to these 9 key genes, of which 4 transcription factors (Stat3, Trp53, NF-κB1, Sp1) were enriched. CONCLUSION:Stat3, Trp53, NF-κB1, and Sp1 were all related to the development of liver fibrosis, and FBLN5 might be a target for liver fibrosis. IJCEP
Authors: Ning Ding; Ruth T Yu; Nanthakumar Subramaniam; Mara H Sherman; Caroline Wilson; Renuka Rao; Mathias Leblanc; Sally Coulter; Mingxiao He; Christopher Scott; Sue L Lau; Annette R Atkins; Grant D Barish; Jenny E Gunton; Christopher Liddle; Michael Downes; Ronald M Evans Journal: Cell Date: 2013-04-25 Impact factor: 41.582
Authors: Andrea Franceschini; Damian Szklarczyk; Sune Frankild; Michael Kuhn; Milan Simonovic; Alexander Roth; Jianyi Lin; Pablo Minguez; Peer Bork; Christian von Mering; Lars J Jensen Journal: Nucleic Acids Res Date: 2012-11-29 Impact factor: 16.971