Journal: Translational Psychiatry

Article Title: What do DNA methylation studies tell us about depression? A systematic review

doi: 10.1038/s41398-019-0412-y

Figure Lengend Snippet: A summary of selected articles in this systematic review

Article Snippet: 11 , Walker et al. , 2016 , Scotland , 29 , Members of a large family multiply affected by BD and MDD , Case–control , MDD , Whole blood , Sodium bisulphite using the EZ-96 DNA Methylation Kit, bead array using the Infinium HumanMethylation450 BeadChip , Genome-wide , Three DMR regions (promoter region of HOXA5 for hypomethylation, 5’ end of RNF39 for hypermethylation, and promoter and first exon of AGPAT1 and RNF5 for hypo-methylation) , Nominally significant differences in DNA methylation were observed; altered DNA methylation was a potential mechanism for mood disorders.

Techniques: DNA Methylation Assay, Genome Wide, Methylation, Variant Assay, Derivative Assay, Biomarker Discovery, Expressing, Software, Binding Assay, Sequencing, EpiTYPER Assay, Control, CpG Methylation Assay, Enzyme-linked Immunosorbent Assay, Immunoprecipitation, Methylated DNA Immunoprecipitation Sequencing, Real-time Polymerase Chain Reaction, SYBR Green Assay, Medications, Marker

Journal: Computational and Structural Biotechnology Journal

Article Title: i-Modern: Integrated multi-omics network model identifies potential therapeutic targets in glioma by deep learning with interpretability

doi: 10.1016/j.csbj.2022.06.058

Figure Lengend Snippet: Ranking scheme of multi-omics signatures. (A) Copy number variation signatures ranking. (B) Gene expression signatures ranking. (C) DNA methylation signatures ranking. (D) miRNA expression signatures ranking. (E) Protein expression signatures ranking. (F) Somatic mutation signatures ranking.

Article Snippet: We obtained multi-omics glioma datasets, including RNA sequencing data (TPM normalized gene expression quantification), protein expression data (Reverse Phase Protein Array RPPA), miRNA-seq expression data (reads per million for miRNA mapping to miRbase 20), DNA methylation data (Infinium HumanMethylation450 BeadChip), copy number variation data (Affymetrix SNP Array 6.0) and somatic mutation data (DNA sequencing).

Techniques: Biomarker Discovery, Gene Expression, DNA Methylation Assay, Expressing, Mutagenesis

Journal: Journal of Cancer Research and Clinical Oncology

Article Title: Aberrant DNA methylation results in altered gene expression in non-alcoholic steatohepatitis-related hepatocellular carcinomas

doi: 10.1007/s00432-020-03298-4

Figure Lengend Snippet: Scatterplot of the levels of mRNA expression ( a ) and DNA methylation ( b ) of the DCAF4L2 , CKLF , TRIM4 , PRC1 , UBE2C and TUBA1B genes in samples of normal control liver tissue (C) and tumorous tissue (T). a mRNA expression levels were determined by SYBR green-based real-time quantitative PCR analysis. b DNA methylation levels were determined by Infinium assay. The Infinium probe ID for each gene is shown in parentheses. Levels of mRNA expression for all six genes were significantly increased in T samples ( n = 22) relative to C samples ( n = 31), whereas levels of DNA methylation on all ten probes designed for the six genes were significantly decreased in T samples ( n = 22) relative to C samples ( n = 36)

Article Snippet: Recently, single-CpG-resolution genome-wide DNA methylation screening using the Infinium assay (Bibikova et al. ) has been introduced for analysis of various human tissue specimens (Tsumura et al. ; Makabe et al. ).

Techniques: Expressing, DNA Methylation Assay, Control, SYBR Green Assay, Real-time Polymerase Chain Reaction

Journal: Journal of Cancer Research and Clinical Oncology

Article Title: Aberrant DNA methylation results in altered gene expression in non-alcoholic steatohepatitis-related hepatocellular carcinomas

doi: 10.1007/s00432-020-03298-4

Figure Lengend Snippet: Genes showing significant inverse correlations between the levels of mRNA expression and DNA methylation in all of the 75 tissue samples, normal control liver tissue samples ( n = 31 and n = 36 for mRNA expression and DNA methylation quantification, respectively), non-cancerous liver tissue samples ( n = 22) obtained from patients with non-alcoholic steatohepatitis-related hepatocellular carcinomas, and the corresponding cancerous tissue samples ( n = 22) in the present cohort

Article Snippet: Recently, single-CpG-resolution genome-wide DNA methylation screening using the Infinium assay (Bibikova et al. ) has been introduced for analysis of various human tissue specimens (Tsumura et al. ; Makabe et al. ).

Techniques: Expressing, DNA Methylation Assay, Control

Journal: Journal of Cancer Research and Clinical Oncology

Article Title: Aberrant DNA methylation results in altered gene expression in non-alcoholic steatohepatitis-related hepatocellular carcinomas

doi: 10.1007/s00432-020-03298-4

Figure Lengend Snippet: Ordered differences in levels of DNA methylation in normal control liver tissue (C) ( n = 36) and non-cancerous liver tissue (N) ( n = 22) obtained from patients with non-alcoholic steatohepatitis-related hepatocellular carcinomas relative to the corresponding tumorous tissue (T) samples ( n = 22) for the DCAF4L2 ( a ), CKLF ( b ), TRIM4 ( c ), PRC1 ( d ), UBE2C ( e ) and TUBA1B ( f ) genes. P values by Jonckheere–Terpstra trend test are shown in each panel. DNA methylation alterations of such genes in N samples relative to C samples were inherited by or further strengthened in the T samples themselves

Article Snippet: Recently, single-CpG-resolution genome-wide DNA methylation screening using the Infinium assay (Bibikova et al. ) has been introduced for analysis of various human tissue specimens (Tsumura et al. ; Makabe et al. ).

Techniques: DNA Methylation Assay, Control

Journal: Journal of Cancer Research and Clinical Oncology

Article Title: Aberrant DNA methylation results in altered gene expression in non-alcoholic steatohepatitis-related hepatocellular carcinomas

doi: 10.1007/s00432-020-03298-4

Figure Lengend Snippet: DNA methylation levels of the DCAF4L2 ( a ), CKLF ( b ), TRIM4 ( c ), PRC1 ( d ), UBE2C ( e ) and TUBA1B ( f ) genes in samples of viral hepatitis-related hepatocellular carcinoma (HCC) (viral-T) ( n = 36) and non-alcoholic steatohepatitis-related HCC (NASH-T) ( n = 22). Levels of DNA methylation for the DCAF4L2 , CKLF and UBE2C genes in NASH-T samples were not significantly different from those in viral-T samples, whereas levels of DNA methylation for the TRIM4 , PRC1 and TUBA1B genes in NASH-T samples were significantly lower than those in viral-T samples, indicating that DNA hypomethylation of the TRIM4 , PRC1 and TUBA1B genes had occurred specifically during NASH-related hepatocarcinogenesis. P values of < 0.05 are underlined

Article Snippet: Recently, single-CpG-resolution genome-wide DNA methylation screening using the Infinium assay (Bibikova et al. ) has been introduced for analysis of various human tissue specimens (Tsumura et al. ; Makabe et al. ).

Techniques: DNA Methylation Assay

Journal: Journal of Cancer Research and Clinical Oncology

Article Title: Aberrant DNA methylation results in altered gene expression in non-alcoholic steatohepatitis-related hepatocellular carcinomas

doi: 10.1007/s00432-020-03298-4

Figure Lengend Snippet: Correlations between DNA methylation levels, defined as low or high using the 25th percentile methylation levels as cutoff values, for the DCAF4L2 , CKLF , TRIM4 , PRC1 , UBE2C and TUBA1B genes and the clinicopathological parameters of patients with non-alcoholic steatohepatitis-related hepatocellular carcinomas (HCCs)

Article Snippet: Recently, single-CpG-resolution genome-wide DNA methylation screening using the Infinium assay (Bibikova et al. ) has been introduced for analysis of various human tissue specimens (Tsumura et al. ; Makabe et al. ).

Techniques: DNA Methylation Assay, Methylation, Activity Assay