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Besides, more attention was paid to the number and length of links in brain networks, and the clustering partitioning of nodes was unclear. Therefore, minimum spanning tree (MST) analysis and the hierarchical clustering were first used for the depression disease in this study. Resting-state electroencephalogram (EEG) sources were assessed from 15 healthy and 23 major depressive subjects. Then the coherence, MST, and the hierarchical clustering were obtained. In the theta band, coherence analysis showed that the EEG coherence of the MDD patients was significantly higher than that of the healthy controls especially in the left temporal region. The MST results indicated the higher leaf fraction in the depressed group. Compared with the normal group, the major depressive patients lost clustering in frontal regions. 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