Dataset Information

Gene expression profiles and protein-protein interaction network analysis in AIDS patients with HIV-associated encephalitis and dementia.

ABSTRACT: Central nervous system dysfunction is an important cause of morbidity and mortality in patients with human immunodeficiency virus type 1 (HIV-1) infection and acquired immunodeficiency virus syndrome (AIDS). Patients with AIDS are usually affected by HIV-associated encephalitis (HIVE) with viral replication limited to cells of monocyte origin. To examine the molecular mechanisms underlying HIVE-induced dementia, the GSE4755 Affymetrix data were obtained from the Gene Expression Omnibus database and the differentially expressed genes (DEGs) between the samples from AIDS patients with and without apparent features of HIVE-induced dementia were identified. In addition, protein-protein interaction networks were constructed by mapping DEGs into protein-protein interaction data to identify the pathways that these DEGs are involved in. The results revealed that the expression of 1,528 DEGs is mainly involved in the immune response, regulation of cell proliferation, cellular response to inflammation, signal transduction, and viral replication cycle. Heat-shock protein alpha, class A member 1 (HSP90AA1), and fibronectin 1 were detected as hub nodes with degree values >130. In conclusion, the results indicate that HSP90A and fibronectin 1 play important roles in HIVE pathogenesis.

SUBMITTER: Shityakov S

PROVIDER: S-EPMC4655943 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Gene expression profiles and protein-protein interaction network analysis in AIDS patients with HIV-associated encephalitis and dementia.

Shityakov Sergey S Dandekar Thomas T Förster Carola C

HIV/AIDS (Auckland, N.Z.) 20151118

Central nervous system dysfunction is an important cause of morbidity and mortality in patients with human immunodeficiency virus type 1 (HIV-1) infection and acquired immunodeficiency virus syndrome (AIDS). Patients with AIDS are usually affected by HIV-associated encephalitis (HIVE) with viral replication limited to cells of monocyte origin. To examine the molecular mechanisms underlying HIVE-induced dementia, the GSE4755 Affymetrix data were obtained from the Gene Expression Omnibus database ...[more]

PMID: 26604827

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Project description:Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that involves the death of neurons. ALS is associated with many gene mutations as previously studied. In order to explore the molecular mechanisms underlying ALS with C9orf72 mutation, gene expression profiles of ALS fibroblasts and control fibroblasts were subjected to bioinformatics analysis. Genes with critical functional roles can be detected by a measure of node centrality in biological networks. In gene co-expression networks, highly connected genes called as candidate hubs have been associated with key disease-related pathways. Herein, this method was applied to find the hub genes related to ALS disease.Illumina HiSeq microarray gene expression dataset GSE51684 was retrieved from Gene Expression Omnibus (GEO) database which included four Sporadic ALS, twelve Familial ALS and eight control samples. Differentially Expressed Genes (DEGs) were identified using the Student's t test statistical method and gene co-expression networking. Gene ontology (GO) function and KEGG pathway enrichment analysis of DEGs were performed using the DAVID online tool. Protein-protein interaction (PPI) networks were constructed by mapping the DEGs onto protein-protein interaction data from publicly available databases to identify the pathways where DEGs are involved in. PPI interaction network was divided into subnetworks using MCODE algorithm and was analyzed using Cytoscape.The results revealed that the expression of DEGs was mainly involved in cell adhesion, cell-cell signaling, Extra cellular matrix region GO processes and focal adhesion, neuroactive ligand receptor interaction, Extracellular matrix receptor interaction. Tumor necrosis factor (TNF), Endothelin 1 (EDN1), Angiotensin (AGT) and many cell adhesion molecules (CAM) were detected as hub genes that can be targeted as novel therapeutic targets for ALS disease.These analyses and findings enhance the understanding of ALS pathogenesis and provide references for ALS therapy.

Dataset Information

Gene expression profiles and protein-protein interaction network analysis in AIDS patients with HIV-associated encephalitis and dementia.

Publications

Gene expression profiles and protein-protein interaction network analysis in AIDS patients with HIV-associated encephalitis and dementia.

Similar Datasets

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