Identification of Key Genes Controlling Carotenoid Metabolism during Apricot Fruit Development by Integrating Metabolic Phenotypes and Gene Expression Profiles

2021 ◽  
Author(s):  
Weiquan Zhou ◽  
Shirong Zhao ◽  
Min Xu ◽  
Yingying Niu ◽  
Mansur Nasier ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fruit Development ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Metabolic Phenotypes ◽  
Carotenoid Metabolism ◽  
Key Genes

scholarly journals Transcriptome Analyses throughout Chili Pepper Fruit Development Reveal Novel Insights into the Domestication Process

Plants ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 585
Author(s):  
Octavio Martínez ◽  
Magda L. Arce-Rodríguez ◽  
Fernando Hernández-Godínez ◽  
Christian Escoto-Sandoval ◽  
Felipe Cervantes-Hernández ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Fruit Development ◽  
Time Course ◽  
Expression Profiles ◽  
Fruit Size ◽  
Gene Expression Profiles ◽  
Chili Pepper ◽  
Time Shift ◽  
The Mean

Chili pepper (Capsicum spp.) is an important crop, as well as a model for fruit development studies and domestication. Here, we performed a time-course experiment to estimate standardized gene expression profiles with respect to fruit development for six domesticated and four wild chili pepper ancestors. We sampled the transcriptomes every 10 days from flowering to fruit maturity, and found that the mean standardized expression profiles for domesticated and wild accessions significantly differed. The mean standardized expression was higher and peaked earlier for domesticated vs. wild genotypes, particularly for genes involved in the cell cycle that ultimately control fruit size. We postulate that these gene expression changes are driven by selection pressures during domestication and show a robust network of cell cycle genes with a time shift in expression, which explains some of the differences between domesticated and wild phenotypes.

scholarly journals Identification of key genes and pathways of BMP-9-induced osteogenic differentiation of mesenchymal stem cells by integrated bioinformatics analysis

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Jia-qi Wu ◽  
Lin-bo Mao ◽  
Ling-feng Liu ◽  
Yong-mei Li ◽  
Jian Wu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Osteogenic Differentiation ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Pathway Enrichment ◽  
Key Genes

Abstract Background The purpose of present study was to identify the differentially expressed genes (DEGs) associated with BMP-9-induced osteogenic differentiation of mesenchymal stem cells (MSCs) by using bioinformatics methods. Methods Gene expression profiles of BMP-9-induced MSCs were compared between with GFP-induced MSCs and BMP-9-induced MSCs. GSE48882 containing two groups of gene expression profiles, 3 GFP-induced MSC samples and 3 from BMP-9-induced MSCs, was downloaded from the Gene Expression Omnibus (GEO) database. Then, DEGs were clustered based on functions and signaling pathways with significant enrichment analysis. Pathway enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) demonstrated that the identified DEGs were potentially involved in cytoplasm, nucleus, and extracellular exosome signaling pathway. Results A total of 1967 DEGs (1029 upregulated and 938 downregulated) were identified from GSE48882 datasets. R/Bioconductor package limma was used to identify the DEGs. Further analysis revealed that there were 35 common DEGs observed between the samples. GO function and KEGG pathway enrichment analysis, among which endoplasmic reticulum, protein export, RNA transport, and apoptosis was the most significant dysregulated pathway. The result of protein-protein interaction (PPI) network modules demonstrated that the Hspa5, P4hb, Sec61a1, Smarca2, Pdia3, Dnajc3, Hyou1, Smad7, Derl1, and Surf4 were the high-degree hub nodes. Conclusion Taken above, using integrated bioinformatical analysis, we have identified DEGs candidate genes and pathways in BMP-9 induced MSCs, which could improve our understanding of the key genes and pathways for BMP-9-induced osteogenic of MSCs.

scholarly journals A Study on Effect of Electroacupuncture on Gene Expression in Hypothalamus of Rats with Stress-Induced Prehypertension Based on Gene Chip Technology

2015 ◽  
Vol 2015 ◽  
pp. 1-12 ◽  
Author(s):  
Xiaojia Xie ◽  
Yan Guo ◽  
Qingguo Liu ◽  
Zhaoyang Wang ◽  
Changqing Guo
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Signal Transduction Pathway ◽  
Gene Expression Profiles ◽  
Gene Chip ◽  
Model Group ◽  
Blank Group ◽  
Chip Technology ◽  
Key Genes ◽  
Model Preparation

Objective. To explore the effect of electroacupuncture (EA) on gene expression in the hypothalamus of rats with stress-induced prehypertension and try to reveal its biological mechanism with gene chip technology.Methods. The stress-induced hypertensive rat model was prepared by combining electric foot-shocks with generated noise. Molding cycle lasted for 14 days and EA intervention was applied on model + EA group during model preparation. Rat Gene 2.0 Array technology was used for the determination of gene expression profiles and the screened key genes were verified by real-time fluorescence quantitative PCR method.Results. Compared with the blank group, 234 genes were upregulated and 73 were downregulated in the model group. Compared with the model group, 110 genes were upregulated and 273 genes were downregulated in model + EA group. The PCR results of the key genes including HSPB1, P2RX4, PPP1R14A, and TH are consistent with that of gene chip test.Conclusion. EA could significantly lower blood pressure of stress-induced prehypertension rats and affect its gene expression profile in hypothalamus. Genes and their signal transduction pathway that related to the contraction of vascular smooth muscle, concentration of Ca2+, and excitability of sympathetic nerve may be involved in EA’s antihypertensive mechanism.

scholarly journals Altered Gene Expression in the Testis of Infertile Patients with Nonobstructive Azoospermia

2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Zhiqiang Wang ◽  
Zhongjun Ding ◽  
Yan Guan ◽  
Chunhui Liu ◽  
Linjun Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Therapeutic Targets ◽  
Gene Expression Profiles ◽  
Enrichment Analysis ◽  
Gene Expression Omnibus ◽  
Nonobstructive Azoospermia ◽  
Coexpression Analysis ◽  
Qrt Pcr ◽  
Key Genes

Background. The molecular mechanism of nonobstructive azoospermia (NOA) remains unclear. The aim of this study was to identify gene expression changes in NOA patients and to explore potential biomarkers and therapeutic targets. Methods. The gene expression profiles of GSE45885 and GSE145467 were collected from the Gene Expression Omnibus (GEO) database, and the differences between NOA and normal spermatogenesis were analyzed. Enrichment analysis was performed to explore biological functions for common differentially expressed genes (DEGs) in GSE45885 and GSE145467. Coexpression analysis of DEGs in GSE45885 was performed, and two modules with the highest correlation with NOA were screened. Key genes were then screened from the intersection genes of the two modules and common DEGs and PPI network. The expression of key genes was validated by quantitative real-time polymerase chain reaction (qRT-PCR) experiments. Finally, through miRTarBase, miRDB, and RAID, the miRNAs were predicted to regulate key genes, respectively. Results. A total of 345 common DEGs were identified and they were mainly related to spermatogenesis, insulin signaling pathway. Coexpression analysis of DEGs in GSE45885 yielded eight modules; MEblack and MEturquoise had the highest correlation with NOA. Six genes in MEturquoise and RNF141 in MEblack were identified as key genes. qRT-PCR experiments validated the differential expression of key genes between NOA and control. Furthermore, RNF141 was regulated by the largest number of miRNAs. Conclusion. Our findings suggest that the significant change expression of key genes may be potential markers and therapeutic targets of NOA and may have some impact on the development of NOA.

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