Isolation and analysis of genes mainly expressed in adult mouse heart using subtractive hybridization cDNA library

Kömürcü-Bayrak, Evrim; Ozsait, B.; Erginel-Unaltuna, Nihan

doi:10.1007/s11033-012-1653-5

Cited by 7 publications

(7 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…This indicates that TOF may share common mechanisms with neurodegenerative disorders. However, the association between NDUFB and NDUFS family genes and TOF has seldom been reported, except for NDUFB5, which has been confirmed to be expressed in mouse heart tissues ( 35 ). Despite the lack of direct evidence, previous studies have supported a connection between TOF and neurodegenerative disorders.…”

Section: Discussionmentioning

confidence: 99%

Microarray analysis reveals key genes and pathways in Tetralogy of Fallot

Qiu

Jiang

et al. 2017

Molecular Medicine Reports

View full text Add to dashboard Cite

The aim of the present study was to identify key genes that may be involved in the pathogenesis of Tetralogy of Fallot (TOF) using bioinformatics methods. The GSE26125 microarray dataset, which includes cardiovascular tissue samples derived from 16 children with TOF and five healthy age-matched control infants, was downloaded from the Gene Expression Omnibus database. Differential expression analysis was performed between TOF and control samples to identify differentially expressed genes (DEGs) using Student's t-test, and the R/limma package, with a log2 fold-change of >2 and a false discovery rate of <0.01 set as thresholds. The biological functions of DEGs were analyzed using the ToppGene database. The ReactomeFIViz application was used to construct functional interaction (FI) networks, and the genes in each module were subjected to pathway enrichment analysis. The iRegulon plugin was used to identify transcription factors predicted to regulate the DEGs in the FI network, and the gene-transcription factor pairs were then visualized using Cytoscape software. A total of 878 DEGs were identified, including 848 upregulated genes and 30 downregulated genes. The gene FI network contained seven function modules, which were all comprised of upregulated genes. Genes enriched in Module 1 were enriched in the following three neurological disorder-associated signaling pathways: Parkinson's disease, Alzheimer's disease and Huntington's disease. Genes in Modules 0, 3 and 5 were dominantly enriched in pathways associated with ribosomes and protein translation. The Xbox binding protein 1 transcription factor was demonstrated to be involved in the regulation of genes encoding the subunits of cytoplasmic and mitochondrial ribosomes, as well as genes involved in neurodegenerative disorders. Therefore, dysfunction of genes involved in signaling pathways associated with neurodegenerative disorders, ribosome function and protein translation may contribute to the pathogenesis of TOF.

show abstract

Section: Discussionmentioning

confidence: 99%

Microarray analysis reveals key genes and pathways in Tetralogy of Fallot

Qiu

Jiang

et al. 2017

Molecular Medicine Reports

View full text Add to dashboard Cite

show abstract

“…Among many transcripts, the Midn transcript was previously isolated from a heart-specific SHL and data of our previous work were given elsewhere in detail (Komurcu-Bayrak et al, 2012). Briefly, we analyzed the data from the SHL by comparative screening through nucleotide and protein sequences in a gene database (http://blast.ncbi.nlm.nih.gov/Blast.cgi).…”

Section: Identification Of Midnolin Transcript From a Heartspecific Cmentioning

confidence: 99%

“…In the systematic bioinformatics analysis of our previously established heart-specific subtractive hybridization cDNA library (Komurcu-Bayrak et al, 2012), we detected a clone with 284 nucleotide length sequence that showed 96% homology to the 3'UTR of the mouse Midn gene (NM_021565.1; positions 3402-3682). According to the NCBI and Ensembl databases, the mouse Midn gene has three alternatively spliced transcripts (NM_021565, NM_001305798, and NM_001305799) that differ mainly in their 5' coding region and transcript variant 1 (NM_021565) encoding the longest isoform (NP_067540).…”

Section: Homology Of Shl Clone To Midn Transcriptmentioning

confidence: 99%

“…Subtractive hybridization is a valuable approach in order to determine the differences between cells or tissues at the gene expression level (Diatchenko et al, 1996;Komurcu-Bayrak et al, 2012). To identify heart-specific transcripts, a subtractive hybridization cDNA library (SHL), which was specific to adult BALB/c mouse heart tissue, was constructed in our previous studies (Komurcu-Bayrak et al, 2012). In the next experiments, selected genes form this library were analyzed in embryonic, neonatal, and adult stages (Özsait Selçuk, 2003;Komurcu-Bayrak et.…”

Section: Introductionmentioning

confidence: 99%

“…To identify heart-specific transcripts, a subtractive hybridization cDNA library (SHL), which was specific to adult BALB/c mouse heart tissue, was constructed in our previous studies (Komurcu-Bayrak et al, 2012). In the next experiments, selected genes form this library were analyzed in embryonic, neonatal, and adult stages (Özsait Selçuk, 2003;Komurcu-Bayrak et. al., 2012).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Higher expression level of Bat3 is associated with silencing of theMidn gene in primary mouse cardiomyocytes

Selçuk¹,

Bayrak²,

Erginel-Unaltuna³

2016

Turk J Biol

View full text Add to dashboard Cite

Midnolin (Midn) is a developmentally regulated nucleolar protein that was originally identified in the mesencephalon of developing mouse embryos. Additionally, Midn expression was detected in various adult tissues and was associated with glucokinase activity in pancreatic beta cells and with the regulation of folliculogenesis in ovaries. In this study, our aim was to analyze the expression and function of the Midn gene in cardiomyocyte cells. We constructed a primary neonatal mouse cardiomyocyte cell culture and analyzed the expression of possible Midn-associated genes after short interfering RNA (siRNA)-mediated gene silencing for Midn. After 24 h of silencing, we observed that the expression level of Bat3 was significantly increased (1.69-fold, P = 0.04). As a result, we have detected a suggestive gene that might act in the common cellular pathways with Midn in cardiomyocyte cells.

show abstract

Identification of Differently Expressed Genes and Small Molecule Drugs for Tetralogy of Fallot by Bioinformatics Strategy

Chen

Xiao

et al. 2014

Pediatr Cardiol

View full text Add to dashboard Cite

This study aimed to screen out differentially expressed genes (DEGs) and explore small molecule drugs for Tetralogy of Fallot (TOF). The gene expression profile of TOF GSE26125 was downloaded from the Gene Expression Omnibus database, including 16 idiopathic TOF samples and five healthy controls. The DEGs were identified by the Limma package in R language and underwent functional enrichment analysis via Database for Annotation, Visualization and Integrated Discovery tools. A protein-protein interaction (PPI) network of DEGs was then constructed and the significant clusters were selected for functional analysis. In addition, the DEGs were mapped to the connectivity map (CMap) database to identify potential small-molecule drugs. As a result, a total of 499 DEGs were selected between TOF and healthy controls. Meanwhile, the functional changes of DEGs related to TOF were mainly associated with cellular respiration and energy metabolism. Furthermore, in the PPI network, two clusters were identified via cluster 1 analysis. And only cluster 1 was significantly enriched into gene ontology terms, including respiratory chain, electron transport chain, and oxidation reduction. The hub gene of cluster 1 was NDUFAB1. Additionally, small molecules, such as harmine, solanine, and testosterone, may have the potential to repair the disordered metabolic pathways of TOF.

show abstract

Isolation and analysis of genes mainly expressed in adult mouse heart using subtractive hybridization cDNA library

Cited by 7 publications

References 34 publications

Microarray analysis reveals key genes and pathways in Tetralogy of Fallot

Microarray analysis reveals key genes and pathways in Tetralogy of Fallot

Higher expression level of Bat3 is associated with silencing of theMidn gene in primary mouse cardiomyocytes

Identification of Differently Expressed Genes and Small Molecule Drugs for Tetralogy of Fallot by Bioinformatics Strategy

Contact Info

Product

Resources

About