Bioinformatics analysis of time series gene expression in left ventricle (LV) with acute myocardial infarction (AMI).
This study is to investigate the key genes and their possible function in acute myocardial infarction (AMI). The data of GSE4648 downloaded from the Gene Expression Omnibus (GEO) database include 6 time points (15 min, 60 min, 4h, 12h, 24h and 48 h) of 12 left ventricle (LV) samples, 12 surviving LV free wall (FW) samples, 12 inter-ventricular septum (IVS) samples after AMI operation and corresponding sham-operated samples. The data of each sample were analyzed with Affy and Bioconductor packages, and differentially expressed genes (DEGs) were screened out using BETR package with false discovery rate (FDR)<0.01. Then, functional enrichment analysis for DEGs was conducted with Database for Annotation, Visualization and Integrated Discovery (DAVID). Totally 194 DEGs were identified in LV, and only the gene tubulin beta 2a (Tubb2a) and natriuretic peptide B (Nppb) were respectively up-regulated in surviving FW tissue and IVS tissue. The biological process response to wounding and inflammatory response were significantly enriched, as well as leukocyte transendothelial migration pathway. Besides, the expression pattern analysis showed the DEGs mostly up-regulated at 4h after AMI, and these genes were mainly associated with immunity. Additionally, in transcriptional regulatory network, early growth response 1 (Egr1), activating transcription factor 3 (Atf3), Atf4, Myc and Fos were considered as the key transcription factors related to immune response. The key transcription factors and potential target genes might provide new information for the development of AMI, and leukocyte transendothelial migration pathway might play a vital role in AMI.
Department of Cardiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin 150001, Heilongjiang Province, China.
Tong
T
Zhang
Department of Gastroenterology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin 150001, Heilongjiang Province, China.
Li-Li
LL
Zhao
Department of Cardiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin 150001, Heilongjiang Province, China.
Xue
X
Cao
Department of Cardiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin 150001, Heilongjiang Province, China.
Li-Chun
LC
Qi
Department of Cardiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin 150001, Heilongjiang Province, China.
Guo-Qian
GQ
Wei
Department of Cardiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin 150001, Heilongjiang Province, China.
Jun-Yan
JY
Liu
Department of Cardiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin 150001, Heilongjiang Province, China.
Shu-Jun
SJ
Yan
The Central Hospital of the Heilongjiang Prison Administrative Bureau, Harbin 150001, Heilongjiang Province, China.
Jin-Gang
JG
Liu
Department of Cardiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin 150001, Heilongjiang Province, China. Electronic address: xueqili89856@hotmail.com.
Xue-Qi
XQ
Li
D019295:Computational Biology; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D006352:Heart Ventricles / Q000378:metabolism*; D006801:Humans; D009203:Myocardial Infarction / Q000235:genetics*; D013997:Time Factors; D014158:Transcription, Genetic
Acute myocardial infarction; Differentially expressed genes; Left ventricle; Time series; Transcription factor