Identifying novel glioma associated pathways based on systems biology level meta-analysis

Abstract

BackgroundWith recent advances in microarray technology, including genomics, proteomics, and metabolomics, it brings a great challenge for integrating this "-omics" data to analysis complex disease. Glioma is an extremely aggressive and lethal form of brain tumor, and thus the study of the molecule mechanism underlying glioma remains very important. To date, most studies focus on detecting the differentially expressed genes in glioma. However, the meta-analysis for pathway analysis based on multiple microarray datasets has not been systematically pursued.ResultsIn this study, we therefore developed a systems biology based approach by integrating three types of omics data to identify common pathways in glioma. Firstly, the meta-analysis has been performed to study the overlapping of signatures at different levels based on the microarray gene expression data of glioma. Among these gene expression datasets, 12 pathways were found in GeneGO database that shared by four stages. Then, microRNA expression profiles and ChIP-seq data were integrated for the further pathway enrichment analysis. As a result, we suggest 5 of these pathways could be served as putative pathways in glioma. Among them, the pathway of TGF-beta-dependent induction of EMT via SMAD is of particular importance.ConclusionsOur results demonstrate that the meta-analysis based on systems biology level provide a more useful approach to study the molecule mechanism of complex disease. The integration of different types of omics data, including gene expression microarrays, microRNA and ChIP-seq data, suggest some common pathways correlated with glioma. These findings will offer useful potential candidates for targeted therapeutic intervention of glioma.

Anthocyanidins inhibit epithelial–mesenchymal transition through a TGFβ/Smad2 signaling pathway in glioblastoma cells

“…TGF‐β can activate EMT in GBM via a Smad‐dependent and a Smad‐independent pathway . The most important of these, the Smad2/3 pathway, plays a predominant role in TGF‐β‐induced EMT in glioblastoma cell lines . Here, we have shown that Cy, Dp, Pg, and Pt attenuated TGF‐β‐induced phosphorylation of Smad2 in a dose‐dependent manner.…”

Gastric Cancer Associated Genes Identified by an Integrative Analysis of Gene Expression Data

“…Hundreds of gene expression profiles and diagnostic targets are uploaded into various gene expression databases. These data can be further integrated to the understanding of the complexity of the diseases, such as the cancer heterogeneity, high level consensus [ 11 – 13 ], biomarker discovery [ 14 , 15 ], and the key players in the cancer genesis and progress [ 16 ]. In this study, we used meta-analysis approach for analysis of multiple transcriptomic datasets.…”

Construction and analysis of dynamic transcription factor regulatory networks in the progression of glioma

“…Therefore, the abnormal expression of single genes may be better viewed collectively at the molecualr network level 18 . In addition, in contrast to single gene/protein targets for the treatment of glioma, these networks establish broader, multi-target pathways for glioma therapy 19 . In contrast to the entire transcription regulatory network, the subnetworks are formed by interactions among the TFs that are expressed in a given cell type, and these subnetworks make the cell system nimble and robust 20 .…”