WEGO (Web Gene Ontology Annotation Plot), created in 2006, is a simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation results. Owing largely to the rapid development of high-throughput sequencing and the increasing acceptance of GO, WEGO has benefitted from outstanding performance regarding the number of users and citations in recent years, which motivated us to update to version 2.0. WEGO uses the GO annotation results as input. Based on GO’s standardized DAG (Directed Acyclic Graph) structured vocabulary system, the number of genes corresponding to each GO ID is calculated and shown in a graphical format. WEGO 2.0 updates have targeted four aspects, aiming to provide a more efficient and up-to-date approach for comparative genomic analyses. First, the number of input files, previously limited to three, is now unlimited, allowing WEGO to analyze multiple datasets. Also added in this version are the reference datasets of nine model species that can be adopted as baselines in genomic comparative analyses. Furthermore, in the analyzing processes each Chi-square test is carried out for multiple datasets instead of every two samples. At last, WEGO 2.0 provides an additional output graph along with the traditional WEGO histogram, displaying the sorted P-values of GO terms and indicating their significant differences. At the same time, WEGO 2.0 features an entirely new user interface. WEGO is available for free at http://wego.genomics.org.cn.
BACKGROUND
Mycoplasma pneumoniae pneumonia (MPP) is an acute respiratory infectious pneumonia with pulmonary interstitial fibrosis. TGF-β1 is well accepted as the central mediator for fibrosis which promotes the formation of tissue fibrosis factor. Qinbaiqingfei pellet (Qinbai) has already been approved as the first effective new traditional Chinese medicine which can delay activities of Mycoplasma pneumoniae (M.pneumoniae) and protect lung epithelial cells in clinical trials. However, the mechanism of Qinbai inhibiting the expression of TGF-β1 is still unclear.
METHODS
The Chinese herbs in Qinbai were screened by surface plasmon resonance (SPR) and it was deteimined that Scutellaria baicalensis extracts in Qinbai showed the best binding with TGF-β1. Then the active ingredient whicn can be bound with TGF-β1 protein in the solution of Qinbai and Scutellaria baicalensis was isolated and analyzed by UPLC-Q-TOF-MS, which proved the active ingredient was Wogonoside. The affinity constant of Wogonoside and TGF-β1 protein was measured by SPR affinity analysis. A549 cells infected with M.pneumoniae were intervened by Wogonoside, and then the expression of TGF-β1 and Smad3 in A549 cells were analyzed by PCR and western blotting.
RESULTS
The results showed the bound effect of Scutellaria baicalensis and TGF-β1 was effective. The active ingredients which can be bound with TGF-β1 in the solution of Scutellaria baicalensis and Qinbai were obtained and analyzed to investigate the mechanism of Qinbai inhibiting the expression of TGF-β1. UPLC-Q-TOF-MS results showed that the active ingredients was Wogonoside. SPR affinity analysis showed that the affinity constant was 21.71 µM. Pharmacological experiments revealed that Wogonoside strongly inhibited the expression of TGF-β1 and Smad3 in A549 cells infected by M.pneumoniae.
CONCLUSION
Wogonoside in Qinbai can be bound with TGF-β1 and down-regulate the expression of lung fibrosis factors TGF-β1 and Smad3. The finding may improve our understanding the molecular mechanism of Qinbai mediating MPP and provide new sights into the future pharmacological investigation of Qinbai.
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