Background Everlasting cellular proliferation is the fundamental feature during gliomagenesis and Ki-67 is one of the classical proliferation markers in human glioblastoma multiforme (GBM).However,the driver genes or core pathways for cellular proliferation in GBM have not been elucidated systematically.Methods We evaluated by immunohistochemistry the prognostic value of Ki-67 expression in the clinical outcome of 156 Chinese patients with GBM and a total of 64 GBM samples were selected for further Agilent genome-wide microarray analysis.On the basis of the microarray data from Tiantan (n=64) and The Cancer Genome Atlas (TCGA) (n=202)database,differentially expressed genes between the GBM subgroups with high or low level of Ki-67 expression were identified using Significance Analysis of Microarrays (SAM).Gene Ontology (GO) and KEGG Pathway analyses were then undertaken for the Ki-67 associated genes to identify the most significant biological processes and signaling pathways.Results We confirmed that Ki-67 was an independent prognostic indicator in the largest Chinese patient cohort of 156 GBM samples via immunohistochemical staining.Survival analysis of Ki-67 over-expression revealed a highly significant association with a worse clinical outcome (P=0.010 for progression-free survival;P=0.007 for overall survival).Comparative and integrated analysis between Tiantan and TCGA database identified a 247-gene "proliferation signature"(205 up-regulated and 42 down-regulated genes) that distinguished Ki-67 expression phenotypes.GO and KEGG Pathway analyses further indicated that Ki-67 expression phenotype was associated with distinct changes in gene expression associated with the regulation of cellular growth and proliferation.Conclusions Proliferation marker Ki-67 is an independent prognostic indicator in Chinese GBM patients.And Ki-67 associated proliferation signature identified through genome-wide microarray analysis may provide potential targets for anti-proliferation therapy in GBM.