scholarly journals GenoExp: a web tool for predicting gene expression levels from single nucleotide polymorphisms

2015 ◽  
Vol 31 (11) ◽  
pp. 1848-1850 ◽  
Author(s):  
Ohad Manor ◽  
Eran Segal
Keyword(s):  
Gene Expression ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Web Tool ◽  
Single Nucleotide ◽  
Expression Levels ◽  
Gene Expression Levels

scholarly journals Asymmetric Divergence in Transmitted SNPs of DNA Replication/Transcription and Their Impact on Gene Expression in Polyploid Brassica napus

2021 ◽  
Vol 12 ◽  
Author(s):  
Minqiang Tang ◽  
Juanling Li ◽  
Xu Hu ◽  
Lu Sun ◽  
MMU Helal ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Replication ◽  
Brassica Napus ◽  
Genome Evolution ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Expression Levels ◽  
Dna And Rna ◽  
Polyploid Genome ◽  
Gene Expression Levels

The marked increase in plant genomic data has provided valuable resources for investigating the dynamic evolution of duplicate genes in polyploidy. Brassica napus is an ideal model species for investigating polyploid genome evolution. The present study comprehensively analyzed DNA and RNA variation of two representative B. napus inbredlines, Zhongshuang11 and Zhongyou821, and we investigated gene expression levels of An and Cn subgenomes in multiple tissues of the two lines. The distribution of transmitted single nucleotide polymorphisms (SNPs) was significantly different in two subgenomes of B. napus. Gene expression levels were significantly negatively correlated with number of variations in replication and transcription of the corresponding genes, but were positively correlated with the ratios of transmitted SNPs from DNA to RNA. We found a higher density of SNP variation in An than that in Cn during DNA replication and more SNPs were transmitted to RNA during transcription, which may contribute to An expression dominance. These activities resulted in asymmetrical gene expression in polyploid B. napus. The SNPs transmitted from DNA to RNA could be an important complement feature in comparative genomics, and they may play important roles in asymmetrical genome evolution in polyploidy.

scholarly journals The role of 25-hydroxyvitamin-D3 and vitamin D receptor gene in human periodontal ligament fibroblasts as response to orthodontic compressive strain: an in vitro study

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Erika Calvano Küchler ◽  
Agnes Schröder ◽  
Vinicius Broska Teodoro ◽  
Ute Nazet ◽  
Rafaela Scariot ◽  
...  
Keyword(s):  
Gene Expression ◽  
Vitamin D ◽  
Single Nucleotide Polymorphisms ◽  
Periodontal Ligament ◽  
Compressive Strain ◽  
Nucleotide Polymorphisms ◽  
Periodontal Ligament Fibroblasts ◽  
Single Nucleotide ◽  
Cox 2

Abstract Background This study aimed to investigate, if different physiological concentrations of vitamin D (25(OH)D3) and single nucleotide polymorphisms in vitamin D receptor (VDR) gene have an impact on gene expression in human periodontal ligament (hPDL) fibroblasts induced by simulated orthodontic compressive strain. Methods A pool of hPDL fibroblasts was treated in absence or presence of 25(OH)D3 in 3 different concentrations (10, 40 and 60 ng/ml). In order to evaluate the role of single nucleotide polymorphisms in the VDR gene, hPDL fibroblasts from 9 patients were used and treated in absence or presence of 40 ng/ml 25(OH)D3. Each experiment was performed with and without simulated orthodontic compressive strain. Real-time PCR was used for gene expression and allelic discrimination analysis. Relative expression of dehydrocholesterol reductase (DHCR7), Sec23 homolog A, amidohydrolase domain containing 1 (AMDHD1), vitamin D 25-hydroxylase (CYP2R1), Hydroxyvitamin D-1-α hydroxylase, receptor activator of nuclear factor-κB ligand (RANKL), osteoprotegerin (OPG), cyclooxygenase-2 (COX-2) and interleukin-6 (IL6) was assessed. Three single nucleotide polymorphisms in VDR were genotyped. Parametric or non-parametric tests were used with an alpha of 5%. Results RANKL, RANKL:OPG ratio, COX-2, IL-6, DHCR7, CYP2R1 and AMDHD1 were differentially expressed during simulated orthodontic compressive strain (p < 0.05). The RANKL:OPG ratio was downregulated by all concentrations (10 ng/ml, 40 ng/ml and 60 ng/ml) of 25(OH)D3 (mean = 0.96 ± 0.68, mean = 1.61 ± 0.66 and mean = 1.86 ± 0.78, respectively) in comparison to the control (mean 2.58 ± 1.16) (p < 0.05). CYP2R1 gene expression was statistically modulated by the different 25(OH)D3 concentrations applied (p = 0.008). Samples from individuals carrying the GG genotype in rs739837 presented lower VDR mRNA expression and samples from individuals carrying the CC genotype in rs7975232 presented higher VDR mRNA expression (p < 0.05). Conclusions Simulated orthodontic compressive strain and physiological concentrations of 25(OH)D3 seem to regulate the expression of orthodontic tooth movement and vitamin-D-related genes in periodontal ligament fibroblasts in the context of orthodontic compressive strain. Our study also suggests that single nucleotide polymorphisms in the VDR gene regulate VDR expression in periodontal ligament fibroblasts in the context of orthodontic compressive strain.

Identifying novel biomarkers of gastric cancer through integration analysis of single nucleotide polymorphisms and gene expression profile

2015 ◽  
Vol 30 (3) ◽  
pp. 321-326 ◽  
Author(s):  
Tao Wang ◽  
Yan Xu ◽  
Peng Hou
Keyword(s):  
Gene Expression ◽  
Gastric Cancer ◽  
Transcription Factor ◽  
Single Nucleotide Polymorphisms ◽  
Gene Expression Omnibus ◽  
Trend Test ◽  
Nucleotide Polymorphisms ◽  
Functional Variation ◽  
Single Nucleotide ◽  
Normal Controls

Purpose Single nucleotide polymorphisms (SNPs) are an important cause of functional variation in proteins leading to tumorigenesis. We aimed to identify candidate biomarkers with polymorphisms in gastric cancer (GC). Methods The SNP microarray profile GSE29996 including 50 GC samples and 50 normal controls, and gene expression data GSE56807 consisting of 5 GC samples and 5 controls were downloaded from the Gene Expression Omnibus database. After preprocessing of raw data, GC-associated SNPs were identified using the Cochran-Armitage trend test, and differentially expressed genes (DEGs) were screened out using the limma package in R. Significant DEGs with risk associated SNP loci were screened using the Fisher combination test. Gene ontology function and pathway enrichment analyses were performed for DEGs with risk associated SNP loci by GenCLip online tool. Transcriptional regulatory analysis was also conducted for transcription factor and target DEGs. Results A total of 79 DEGs with risk associated SNP loci were identified from GC samples compared with normal controls. These DEGs were mainly enriched in anatomical structure development, including embryo development. Additionally, DEGs were significantly involved in the NO1 pathway, including actin, alpha 1, skeletal muscle (ACTA1). In the regulatory network, transcription factor forkhead box L1 (FOXL1) regulated 26 DEGs with risk associated SNP loci, including Iroquois homeobox 1 (IRX1) rs11134044, sex determining region Y (SRY)-box1 (SOX1) rs9549447 and msh homeobox 1 (MSX1) rs41451149. Conclusions IRX1, SOX1 and MSX1 with risk associated SNP loci may serve as candidate biomarkers for diagnosis and prognosis of GC.

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