Dataset Information

Gene expression profile analysis in epilepsy by using the partial least squares method.

ABSTRACT: PURPOSE: Epilepsy is a common chronic neurological disorder. We aim to investigate the underlying mechanism of epilepsy with partial least squares- (PLS-) based gene expression analysis, which is more sensitive than routine variance/regression analysis. METHODS: Two microarray data sets were downloaded from the Gene Expression Omnibus (GEO) database. PLS analysis was used to identify differentially expressed genes. Gene ontology and network analysis were also implemented. RESULTS: A total of 752 genes were identified to be differentially expressed, including 575 depressed and 177 overexpressed genes in patients. For GO enrichment analysis, except for processes related to the nervous system, we also identified overrepresentation of dysregulated genes in angiogenesis. Network analysis revealed two hub genes, CUL3 and EP300, which may serve as potential targets in further therapeutic studies. CONCLUSION: Our results here may provide new understanding for the underlying mechanisms of epilepsy pathogenesis and will offer potential targets for producing new treatments.

SUBMITTER: Wang D

PROVIDER: S-EPMC4052702 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Gene expression profile analysis in epilepsy by using the partial least squares method.

Wang Dong D Song Xixiao X Wang Yan Y Li Xia X Jia Shanshan S Wang Zhijing Z

TheScientificWorldJournal 20140512

<h4>Purpose</h4>Epilepsy is a common chronic neurological disorder. We aim to investigate the underlying mechanism of epilepsy with partial least squares- (PLS-) based gene expression analysis, which is more sensitive than routine variance/regression analysis.<h4>Methods</h4>Two microarray data sets were downloaded from the Gene Expression Omnibus (GEO) database. PLS analysis was used to identify differentially expressed genes. Gene ontology and network analysis were also implemented.<h4>Results ...[more]

PMID: 24959624

Similar Datasets

Project description:In metabolomics, identification of metabolic pathways altered by disease, genetics, or environmental perturbations is crucial to uncover the underlying biological mechanisms. A number of pathway analysis methods are currently available, which are generally based on equal-probability, topological-centrality, or model-separability methods. In brief, prior identification of significant metabolites is needed for the first two types of methods, while each pathway is modeled separately in the model-separability-based methods. In these methods, interactions between metabolic pathways are not taken into consideration. The current study aims to develop a novel metabolic pathway identification method based on multi-block partial least squares (MB-PLS) analysis by including all pathways into a global model to facilitate biological interpretation. The detected metabolites are first assigned to pathway blocks based on their roles in metabolism as defined by the KEGG pathway database. The metabolite intensity or concentration data matrix is then reconstructed as data blocks according to the metabolite subsets. Then, a MB-PLS model is built on these data blocks. A new metric, named the pathway importance in projection (PIP), is proposed for evaluation of the significance of each metabolic pathway for group separation. A simulated dataset was generated by imposing artificial perturbation on four pre-defined pathways of the healthy control group of a colorectal cancer study. Performance of the proposed method was evaluated and compared with seven other commonly used methods using both an actual metabolomics dataset and the simulated dataset. For the real metabolomics dataset, most of the significant pathways identified by the proposed method were found to be consistent with the published literature. For the simulated dataset, the significant pathways identified by the proposed method are highly consistent with the pre-defined pathways. The experimental results demonstrate that the proposed method is effective for identification of significant metabolic pathways, which may facilitate biological interpretation of metabolomics data.

Dataset Information

Gene expression profile analysis in epilepsy by using the partial least squares method.

Publications

Gene expression profile analysis in epilepsy by using the partial least squares method.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets