| 1. BackgroundThe classical theory of TCM "same Zheng existing in the different diseases" suggests that there may be a correlation between the comprehensive clinical manifestation of TCM "Zheng" and the diseases of Western medicine. But the clinical diagnosis and the use of traditional Chinese herbs for "Zheng", can not fully apply with the standard of Western medicine, but using the clinical diagnosis and treatment with TCM characteristics. Therefore, the clinical researches based on TCM Zheng have a rapid development, which covers a very wide range. However, most of them were releted to the traditional clinical evaluation, and the studies using new technology and multidisciplinary were insufficient. In this study, using the technology of network pharmacology, molecular biology and other related subjects, we will constructe and compare the gene networks among the QiXuXueYu Zheng and its related diseases, and put forward a network analysis method based on GO enrichment of function module to explore the correlation between Zheng and diseases, which will provide a new idea for clinical use and development of TCM Zheng.2. AimOur study takes a Common TCM Zheng, QiXuXueYu Zheng, for example, after constructing an integrated gene network of QiXuXueYu Zheng symptoms and their associated diseases, we will compare the similarities and differences of the GO function and KEGG pathways of the function modules among the QiXuXueYu Zheng symptoms and their associated diseases gene networks, in order to reveal the potential mechanism of the TCM theory "same Zheng existing in different diseases". Meanwhile, we also aim to provide a new approach to the research and development of new drug for Zheng by filtering the most relative herb for the gene network of QiXuXueYu Zheng and the related diseases via relevant literature retrieval.3. Material and methods3.1 Getting the data of QiXuXueYu Zheng and the related diseasesAccording to the effect of Yi-Qi-Tong-Luo to heart, brain, kidney and the pathological changes caused by QiXuXueYu Zheng. Retrieval clinical research journal literature of QiXuXueYu Zheng, and analyzed the typical symptoms of QiXuXueYu Zheng which based on CNKI and WanFang electronic data. Using OMIM database to find the deficiency of QiXuXueYu Zheng and the related genes of three diseasedisease (cerebral infarction, angina pectoris, diabetes kidney).3.2 Constructing gene networksWe builded the overlapping and unique gene networks of QiXuXueYu Zheng and associated with three diseases by using the agilent literature retrieval software. And the data was visualized and analyzed the networks topology (clustering coefficient, the number of nodes, the network diameter, the network centricity, radius, etc) via Cytoscape software.3.3 Identification of functional modulesUsing MCODE clustering analysis method for module partition and analyzing their module’s attributes for overlapping genes and networks. In order to get more reliable module, we calculate the minimum entropy module, and also take the visualization for module by Cytoscape software.3.4 Biological function annotation for network modulesThe biological function modules were enriched analysis with DAVID software and chosed the Functional Annotation Chart which mainly for the GO biological functions and KEGG signaling pathways(background:human genome-wide data, P< 0.05).3.5 Analysis of the correlation between related genes and herbsBased on the overlapping/unique genes of QiXuXueYu Zheng and related diseases, we searched the related Chinese herbs in PubMed. Set the key words as "gene name" and "herb", search scope defined for the title or abstract, read the retrieved literature full text and determine the Chinese herbs which were related to the genes. And calculated the correlation coefficient and determined the herbs that were most closely associated with the disease.3.6 Literature verificationIn order to verifing the important results of this study and finding the new biological pathways of QiXuXueYu Zheng and related diseases. We have carried out a large amount of literature validation on all the results of this study. Then the retrieved data were read and found the research reports which were consistent with the results of this study.4. Result4.1 Diseases of QiXuXueYu ZhengAccording to the inclusion and exclusion criteria, read the full text of 10796 literatures screened with highest frequency and belong to the QiXuXueYu Zheng. And 261,255 and 9 were related to cerebral infarction, angina pectoris and diabetic nephropathy.4.2 Symptoms of QiXuXueYu ZhengThrough read the full text of QiXuXueYu Zheng and standardized,3 typical symptoms of disease were getted after finishing (frequency≥2). In all 18 symptoms, the top five symptoms are:dim tongue, shortness of breath, fatigue, pulse, chest pain, dark complexion.4.3 Constructed gene interaction network4.3.1 Related genes of QiXuXueYu Zheng and three diseasesThere are 13 symptoms in the OMIM database has been found 1867 related genes, and 194,113 and 129 genes were related to cerebral infarction, angina pectoris and diabetic nephropathy.4.3.2 Construction of overlapping genes and unique gene networksIn the overlapping genes network of QiXuXueYu Zheng and related diseases,189 nodes and 401 strip edges were related to cerebral infarction 314 nodes and 738 edges were relevant to angina pectoris and 140 nodes and 259 edges were related with diabetic nephropathy. In the unique genes network,269 nodes and 505 edges were related to cerebral infarction,271 nodes and 1015 edges were relevant to angina pectoris and 381 nodes and 3253 edges were related with diabetic nephropathy. And 1104 nodes and 13472 strip edges were revelant to Zheng.4.4 Recognition result of function moduleIn the function modules of overlapping genes network,34,17 and 23 were related to cerebral infarction, angina pectoris and diabetic nephropathy. In the function modules of unique genes network,39,25 and 41 were related to cerebral infarction, angina pectoris and diabetic nephropathy. At the same time, analyzed the number of minimum module and network of module.4.5 Biological function enrichment analysis results of moduleIn the overlapping genes, cerebral infarction contained 617 Go functions and 65 KEGG pathways, angina pectoris had 404 Go functions and 32 KEGG pathways and diabetic nephropathy had 281 Go functions and 26 KEGG pathways. In thea unique genes, cerebral infarction had 48 Go functions and 12 KEGG pathways, angina pectoris had 174 Go functions and 38 KEGG pathways and diabetic nephropathy had 372 Go functions and 26 KEGG pathways. And 1165 Go functions and 58 KEGG pathways were belong to Zheng.4.6 Potential herbs corralted to the related genesFound that frequency>2 and JKD similarity coefficient of the largest Chinese herbs including astragalus root, ginseng, twotooth achyranthes root. Unique genes found that the Chinese herbs including astragalus root, angelica, safflower, creat, epimedium, notoginseng, cinnamon, ginseng, purslane, tripterygium wilfordii, artemisinin. Purslane, tripterygium wilfordii and artemisia annua in traditional Chinese herbs formula are rarely used in clinical treatment of related diseases of QiXuXueYu Zheng.4.7 ValidationOverlapping genes functional modules are enriched in the KEGG pathway,65,32 and 26 were related to brain infarction, angina pectoris and diabetic nephropathy. It is proved that the 3 KEGG pathways has not been reported related to the diseases, and allograft rejection and QiXuXueYu Zheng of three diseases most closely.5. Conclusion1.Through analysis the gene networks, and modular biological function, we found there was a common pathological mechanism of vascular tone converting enzyme between QiXuXueYu Zheng and cerebral infarction, angina pectoris and diabetic nephropathy, partly verify the theory of "same Zheng existing in different diseases" in TCM.2. Based on the classical theory of "same Zheng existing in different diseases" in TCM, we provide a new reseach mode for Zheng by network module analysis.3. The method to the novel finding on the 3 Chinese herbs(Portulaca oleracea, Tripterygium wilfordii, Artemisia annua L.) for QiXuXueYu Zheng gene network, may provide a new approach to the research and development of new drug for Zheng. |
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