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Screening of Key Genes Associated with Ischemic Stroke via Microarray Data

Published online by Cambridge University Press:  23 September 2014

Jianmin Wang ,
Dongliang Zhou ,
Hongwei Qin ,
Ying Xu ,
Ying Guan  and
Weidong Zang
Jianmin Wang*
Affiliation:
Department of Neurology, Baoshan Branch of Huashan Hospital, Fudan University
Dongliang Zhou
Affiliation:
Department of Neurology, Baoshan Branch of Huashan Hospital, Fudan University
Hongwei Qin
Affiliation:
Department of Neurology, Baoshan Branch of Huashan Hospital, Fudan University
Ying Xu
Affiliation:
Department of Neurology, Baoshan Branch of Huashan Hospital, Fudan University
Ying Guan
Affiliation:
Department of Neurology, Baoshan Branch of Huashan Hospital, Fudan University
Weidong Zang
Affiliation:
FengHe (ShangHai) Information Technology Co. Ltd., Shanghai, China
*
No. 1999 Changjiang West Road, Shanghai 200431, China. Email: wangjianmin5588885@hotmail.com.
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Abstract

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Objective:

To promote understandings about the pathogenesis of ischemic stroke (IS) through mining key genes, functions and pathways with microarray technology.

Methods:

Differentially expressed genes (DEGs) in blood between patients with IS and healthy people were screened out through comparing microarray data obtained from Gene Expression Omnibus. Overrepresented functions in DEGs were revealed by Gene Ontology (GO) enrichment analysis. Interaction network was constructed for the top 24 DEGs with information from Human Protein Reference Database (HPRD). Relevant microRNAs (miRNAs) were retrieved from three databases: TargetScan, miRBase and miRanda.

Results:

A total of 503 DEGs were obtained. Functional enrichment analysis showed that immune response, signaling pathways and apoptosis were significantly over-represented. Six key genes with big degree, betweenness and clustering coefficient were then revealed, which might play important roles in the development of IS. In addition, 57 differentially expressed miRNAs targeting the 6 genes were retrieved.

Conclusions:

Our study provides insights into the pathogenesis of IS and potential targets to treat the disease.

Résumé

RÉSUMÉObjectif:

Le but de l'étude était de favoriser la compréhension de la pathogenèse de l'accident vasculaire cérébral ischémique (AVCI) en explorant des gènes, des fonctions et des voies de signalisation clés au moyen de la technique des biopuces.

Méthode:

Des gènes différentiellement exprimés (GDE) dans le sang de patients atteints d'un AVCI et de sujets sains ont été étudiés en comparant les données acquises par la technique des micropuces obtenues de Gene Expression Omnibus. Les fonctions surreprésentées dans les GDE ont été identifiées par le test d'enrichissement basé sur le Gene Ontology. Un réseau d'interactions a été construit pour les 24 premiers GDE au moyen d'informations obtenues de la Human Protein Reference Database. Les micro-ARN pertinents ont été obtenus de trois bases de données : TargetScan, miRBase et miRanda.

Résultats:

Nous avons obtenu 503 GDE en tout. L'analyse d'enrichissement fonctionnel a montré que la réponse immunitaire, les voies de signalisation et l'apoptose étaient surrepésentées de façon significative. Six gènes clés ayant un coefficient élevé d'intermédiarité et de clustering ont ensuite été identifiés. Ils pourraient jouer des rôles importants dans la genèse de l'AVCI. De plus, nous avons identifié 57 micro-ARN différentiellement exprimés ciblant les 6 gènes.

Conclusions:

Notre étude fournit des informations sur la pathogenèse de l'AVCI et des cibles potentielles de traitement de la maladie.

Type
Original Article
Information
Canadian Journal of Neurological Sciences , Volume 40 , Issue 6 , November 2013 , pp. 864 - 869
Copyright
Copyright © The Canadian Journal of Neurological 2013

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