Journal: BMC Bioinformatics

Article Title: Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer

doi: 10.1186/s12859-019-2687-7

Figure Lengend Snippet: A screenshot of the results of CMAcorrel for analysis of 5746 CpG loci with correlation coefficients higher then 0.18 (and r < − 0.18) between the levels of DNA methylation and gene expression. We analysed 500 bp regions around each CpG. At the right there is the composite model consisting of two composite modules with 10 PWMs each. At the left there is the plot of DNA-methylation-gene expression correlation versus the composite score of the region around CpG. Spearman correlation coefficient = 0.38. PWMs are the Position Weight Matrices (PWMs) selected by CMAcorrel algorithm to be included into the model consisting of two composite modules. Below each matrix name are the cut-off values given that were optimized by the CMAcorrel algorithm (in cases of cut-off = 0.0 the original profile cut-off was chosen by the algorithm). The parameter N (e.g. N = 2) gives the number of top scoring TF sites in the sequence that were considered for score calculation. The module width is the sigma value of the score (see Methods section)

Article Snippet: DNA and RNA was extracted from these samples and was sent to Institut d’Investigació Biomédica de Bellvitge, Spain (IDIBELL) for DNA methylation analysis (using 450 K Affymetrix microarrays) and to Université de Genève, Switzerland for RNA sequencing.

Techniques: DNA Methylation Assay, Gene Expression, Sequencing

Journal: BMC Bioinformatics

Article Title: Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer

doi: 10.1186/s12859-019-2687-7

Figure Lengend Snippet: The final list of 19 TFs after filtering according to their differential expression as well as differential DNA methylation and the level of correlation with the methylation in the associated CpG loci

Article Snippet: DNA and RNA was extracted from these samples and was sent to Institut d’Investigació Biomédica de Bellvitge, Spain (IDIBELL) for DNA methylation analysis (using 450 K Affymetrix microarrays) and to Université de Genève, Switzerland for RNA sequencing.

Techniques: Quantitative Proteomics, DNA Methylation Assay, Methylation, Control

Journal: BMC Bioinformatics

Article Title: Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer

doi: 10.1186/s12859-019-2687-7

Figure Lengend Snippet: Selected 23 genes as potential master-regulators prioritized according to the level of differential gene expression in different cancer stages and in metastatic cancer and also according to the level of the differential DNA methylation in cancer versus control sets

Article Snippet: DNA and RNA was extracted from these samples and was sent to Institut d’Investigació Biomédica de Bellvitge, Spain (IDIBELL) for DNA methylation analysis (using 450 K Affymetrix microarrays) and to Université de Genève, Switzerland for RNA sequencing.

Techniques: Gene Expression, DNA Methylation Assay, Control

Journal: BMC Bioinformatics

Article Title: Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer

doi: 10.1186/s12859-019-2687-7

Figure Lengend Snippet: Selected set of 47 potential DNA methylation biomarkers

Article Snippet: DNA and RNA was extracted from these samples and was sent to Institut d’Investigació Biomédica de Bellvitge, Spain (IDIBELL) for DNA methylation analysis (using 450 K Affymetrix microarrays) and to Université de Genève, Switzerland for RNA sequencing.

Techniques: DNA Methylation Assay, Methylation, Expressing

Journal: BMC Bioinformatics

Article Title: Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer

doi: 10.1186/s12859-019-2687-7

Figure Lengend Snippet: Diagram of DNA methylation values of two markers cg00163372 (in gene MYC ) and cg08018731 (in gene NOS3 ). The red dots show values obtained in tumor samples, the green dots show values for the normal samples

Article Snippet: DNA and RNA was extracted from these samples and was sent to Institut d’Investigació Biomédica de Bellvitge, Spain (IDIBELL) for DNA methylation analysis (using 450 K Affymetrix microarrays) and to Université de Genève, Switzerland for RNA sequencing.

Techniques: DNA Methylation Assay

Journal: BMC Bioinformatics

Article Title: Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer

doi: 10.1186/s12859-019-2687-7

Figure Lengend Snippet: Six DNA methylation markers selected for building CRC diagnostic classification function using SVM method

Article Snippet: DNA and RNA was extracted from these samples and was sent to Institut d’Investigació Biomédica de Bellvitge, Spain (IDIBELL) for DNA methylation analysis (using 450 K Affymetrix microarrays) and to Université de Genève, Switzerland for RNA sequencing.

Techniques: DNA Methylation Assay, Diagnostic Assay

Journal: Cells

Article Title: Liquid Biopsy in Alzheimer’s Disease Patients Reveals Epigenetic Changes in the PRLHR Gene

doi: 10.3390/cells12232679

Figure Lengend Snippet: DNA methylation levels in the promoter region of PRLHR gene in hippocampus from Alzheimer’s disease (AD) and controls. ( A ) The figure shows the genomic position of the amplicon (black box) validated using bisulfite cloning sequencing which contains the CpG assayed by the Infinium Human Methylation 450K BeadChip array within the promoter region of PRLHR gene. An example of the 19 CpGs composing the amplicon fully methylated (black circles) is shown. Numbers below indicate each CpG position within the amplicon in base pairs. PRLHR is located on the long arm of chromosome 10 (chr10: 120, 352, 916–120, 355, and 160). The CpG island is represented by a green box as shown in the UCSC Genome Browser. ( B ) Dot-plot chart representing 450K methylation levels for PRLHR hippocampal samples. As seen in the figure, a significant increase in DNA methylation was identified between AD patients and controls. ( C ) Dot-plot chart representing 450K methylation levels for PRLHR according to ABC scale. Horizontal lines represent median methylation values and interquartile range for each group. ( D ) Representative examples of bisulfite cloning sequencing validation for the amplicon containing the CpGs are shown. Black and white circles represent methylated and unmethylated cytosines, respectively. Each column indicates every CpG site in the examined amplicon, and each row represents an individual DNA clone. CpG1 (blue) and CpG2 (orange) assessed by pyrosequencing are represented. *** p -value < 0.001, ** p -value < 0.01 (Mann–Whitney U test).

Article Snippet: In this study, we used our previous DNA methylation microarray data obtained by the Infinium Human Methylation 450K BeadChip (450K array) [ ].

Techniques: DNA Methylation Assay, Amplification, Cloning, Sequencing, Methylation, Biomarker Discovery, MANN-WHITNEY

Journal: Cells

Article Title: Liquid Biopsy in Alzheimer’s Disease Patients Reveals Epigenetic Changes in the PRLHR Gene

doi: 10.3390/cells12232679

Figure Lengend Snippet: Scatter plots graphs of Spearman correlation analysis between DNA methylation levels of 450K and p-tau burden ( A ) and β-amyloid deposition ( B ). A significant positive correlation was found between PRLHR methylation and p-tau (r = 0.45; p -value < 0.01) and β-amyloid (r = 0.39; p -value < 0.05) ( n = 24).

Article Snippet: In this study, we used our previous DNA methylation microarray data obtained by the Infinium Human Methylation 450K BeadChip (450K array) [ ].

Techniques: DNA Methylation Assay, Methylation

Journal: Epigenomics

Article Title: Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences

doi: 10.2217/epi.15.114

Figure Lengend Snippet: Venn diagram showing the degree of CpG overlapping (yellow) between the Infinium HumanMethylation450 BeadChip (450K; red) and the MethylationEPIC BeadChip (850K; green) microarrays.

Article Snippet: The MethylationEPIC BeadChip Infinium also interrogates 2880 CNG (C stands for cytosine; N stands for any nucleotide; G stands for guanine) sites that are present in the 450K DNA methylation microarray ( Supplementary Table 4 ), while 211 CNG sites from the 450K microarray are not included in the 850K platform.

Techniques:

Journal: Epigenomics

Article Title: Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences

doi: 10.2217/epi.15.114

Figure Lengend Snippet: Comparison of methylation values from HumanMethylation450 and their corresponding shared CpG sites present on MethylationEPIC microarray (A) for a renal tumor sample (RCC9). Assay reproducibility (B) of methylation measurements when using technical replicates on a normal colon (NC22A) sample. Correlation plot (C) of the methylation values obtained from a FFPE sample (RCC9-FFPE) when compared with its match biopsy of the same tumor that was preserved as FF (RCC9). 5-hmC value representation (D) , where the same sample was treated as per conventional bifsulfite conversion or as per oxBS. Differences on oxBS with bifsulfite conversion are due to the level of 5-hydroxymethylation, where the absence of 5-hmC has been modeled as a discontinue red line. Frequency of hydroxymethylaton values (E) as a result of subtracting the oxBS values (due to 5-mC) from the BS values (due to 5-mC + 5-hmC) for each CpG site included on the 850K array. 5-hmC: 5-hydroxymethylation; FF: Fresh frozen; FFPE: Formalin-fixed paraffin-embedded; oxBS: Oxidative bisulfite conversion.

Article Snippet: The MethylationEPIC BeadChip Infinium also interrogates 2880 CNG (C stands for cytosine; N stands for any nucleotide; G stands for guanine) sites that are present in the 450K DNA methylation microarray ( Supplementary Table 4 ), while 211 CNG sites from the 450K microarray are not included in the 850K platform.

Techniques: Comparison, Methylation, Microarray, Formalin-fixed Paraffin-Embedded

Journal: Epigenomics

Article Title: Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences

doi: 10.2217/epi.15.114

Figure Lengend Snippet: (A) Differentially methylated CpG sites (Δβ ≥0.66 ) on MethylationEPIC BeadChip microarray from a normal colon sample (NC22A), and normal sorted brain neurons (N229). Heatmap representation of differentially methylated CpG sites (left) and methylation values distribution (right) of samples where methylation differences threshold has been denoted as a discontinued red line (Δβ ≥0.66), and those values considered as differentially methylated have been highlighted in blue. (B) Differentially methylated CpG sites (Δβ ≥0.66), among the newly added 413,759 CpG sites of the MethylationEPIC BeadChip microarray, for a normal colon sample (NC22A), and normal sorted brain neurons (N229). Heatmap representation of differentially methylated CpG sites (left) and methylation values distribution (right) of samples where methylation differences threshold has been denoted as a discontinued red line (Δβ ≥0.66), and those values considered as differentially methylated have been highlighted in blue.

Article Snippet: The MethylationEPIC BeadChip Infinium also interrogates 2880 CNG (C stands for cytosine; N stands for any nucleotide; G stands for guanine) sites that are present in the 450K DNA methylation microarray ( Supplementary Table 4 ), while 211 CNG sites from the 450K microarray are not included in the 850K platform.

Techniques: Methylation, Microarray

Journal: Scientific Data

Article Title: The Personal Genome Project-UK, an open access resource of human multi-omics data

doi: 10.1038/s41597-019-0205-4

Figure Lengend Snippet:

Article Snippet: Genomic DNA (500 ng) extracted from whole blood and saliva was bisulfite converted using the EZ DNA Methylation Kit (Zymo Research) following the recommended incubation conditions for 450 k. Methylation profiling was subsequently performed on 450 k arrays using Illumina iScan Microarray Scanner at UCL Genomics, in accordance with standard operating procedures.

Techniques: DNA Methylation Assay, Sequencing, Methylation Sequencing, DNA Sequencing, RNA Sequencing Assay