Journal: Molecular Human Reproduction

Article Title: Immune cell and transcriptomic analysis of the human decidua in term and preterm parturition

doi: 10.1093/molehr/gax038

Figure Lengend Snippet: Sample–sample network graph of microarray data. Normalized expression data for the top up-and down-regulated genes ( P < 0.05, fold change ≥ 1.2) identified by microarray analysis were visualized using BioLayout Express 3D . Each node represents a different patient sample and edges are coloured to reflect the Pearson correlation that they represent. Red edges indicate high correlation, and blue edges represent low correlation. The same data set is used for each graph. ( A ) unbiased MCL cluster (MCLi = 20). ( B ) Nodes are coloured by gestation and labour status into our four sample groups: TNL ( n = 11), TL ( n = 9), PTNL ( n = 7) and PTL ( n = 8).

Article Snippet: Microarray data analysis was performed by Fios Genomics Ltd (Bioquarter, Edinburgh, UK).

Techniques: Microarray, Expressing

Journal: Molecular Human Reproduction

Article Title: Immune cell and transcriptomic analysis of the human decidua in term and preterm parturition

doi: 10.1093/molehr/gax038

Figure Lengend Snippet: QRT-PCR validations of gene expression changes in TL decidua samples. Decidual expression of selected genes identified as significantly elevated in TL in the microarray analysis was examined across our four sample groups by qRT-PCR [TNL ( n = 11), TL ( n = 9), PTNL ( n = 7) and PTL ( n = 10)]. ( A ) IL-6 expression, ( B ) PTGS2 expression, ( C ) IER3 expression, ( D ) TNFAIP3 expression and ( E ) ATF3 expression. Data are presented as mean fold change ± SEM. Data were analysed by one-way ANOVA followed by Tukey post hoc test. * P < 0.05, *** P < 0.001.

Article Snippet: Microarray data analysis was performed by Fios Genomics Ltd (Bioquarter, Edinburgh, UK).

Techniques: Quantitative RT-PCR, Gene Expression, Expressing, Microarray

Journal: Molecular Human Reproduction

Article Title: Immune cell and transcriptomic analysis of the human decidua in term and preterm parturition

doi: 10.1093/molehr/gax038

Figure Lengend Snippet: QRT-PCR validations of gene expression changes in PTL decidua samples. Decidual gene expression of selected genes identified as significantly elevated in PTL samples in the microarray analysis was examined across our four sample groups by qRT-PCR [TNL ( n = 11), TL ( n = 9), PTNL ( n = 7), PTL ( n = 10)]. ( A ) CXCL8 expression, ( B ) MARCO expression, ( C ) LILRA3 expression, ( D ) FGA expression, ( E ) FGB expression, ( F ) FGG expression, ( G ) PLAT expression and ( H ) PLAU expression. Data are presented as mean fold change ± SEM. Data were analysed by one-way ANOVA followed by Tukey post hoc test. * P < 0.05, ** P < 0.01.

Article Snippet: Microarray data analysis was performed by Fios Genomics Ltd (Bioquarter, Edinburgh, UK).

Techniques: Quantitative RT-PCR, Gene Expression, Microarray, Expressing

Journal: PLoS ONE

Article Title: Irisin promotes C2C12 myoblast proliferation via ERK-dependent CCL7 upregulation

doi: 10.1371/journal.pone.0222559

Figure Lengend Snippet: (A) Gene ontology (GO) analysis of irisin-regulated transcriptome in C2C12 cells. The graph shows–log p values (modified Fisher’s exact P -values) obtained from GO analysis in terms of ‘biological processes’ using microarray data [fold change ≥ 2, pooled samples (n = 3) per group]. (B) mRNA expression levels of enriched genes involved in positive regulation of ERK signaling pathway obtained from microarray data. (C) Validation of expression levels of genes involved in positive regulation of ERK cascade ( Ccl2 , Ccl7 , Ccl8 , C3 , and Pdgfa ). Relative mRNA levels were analyzed by qRT-PCR using SYBR Green dye (n = 3 per group).

Article Snippet: For microarray analysis, total RNA was pooled from n = 3 biological replicates and processed in BioCore (Seoul, Republic of Korea) as described below.

Techniques: Modification, Microarray, Expressing, Biomarker Discovery, Quantitative RT-PCR, SYBR Green Assay

Journal: Molecules

Article Title: Insights into the Gene Expression Profile of Classical Hodgkin Lymphoma: A Study towards Discovery of Novel Therapeutic Targets

doi: 10.3390/molecules29153476

Figure Lengend Snippet: Research workflow. This study commenced with the retrieval of gene expression microarray datasets related to cHL and healthy individuals. The data were preprocessed using various statistical tools to obtain the most significant gene expression values. Differentially expressed genes were identified, revealing sets of upregulated and downregulated genes in cHL. Further analysis of the upregulated genes was conducted with respect to their involvement in different pathways using GSEA analysis. Additionally, network analysis was performed on the upregulated genes to identify deep connections among them. Significant interactions were found between the top two upregulated genes, highlighting their effective role in cHL. This hypothesis was validated by further exploring the roles of key genes using reference databases. The analysis identified key genes with significant roles in the progression of cHL. Subsequently, structural analyses were performed, where the three-dimensional protein structure of the target gene was retrieved, minimized, and evaluated for stability. The active site was predicted, and its coordinates were calculated for the grid box setting. Ligands were retrieved and minimized for the docking protocol. Both the ligands and the protein were selected for docking, and the binding potentials were calculated, followed by interaction analysis between the docked entities. Finally, simulations were conducted on the docked complexes to evaluate their behavior, respectively.

Article Snippet: Microarray data analysis was solely performed using R-Studio v4.4.1.

Techniques: Gene Expression, Microarray, Binding Assay