Journal: iScience

Article Title: DNA methylation dynamics associated with long-term isolation of simulated space travel

doi: 10.1016/j.isci.2022.104493

Figure Lengend Snippet:

Article Snippet: The normalized 450k methylation data were downloaded from GeneLab database (GLDS-140), where detailed data normalization flow could be viewed ( ).

Techniques: DNA Methylation Assay, Expressing, Software

Journal: Journal of Clinical Medicine

Article Title: Methylation Status of Corticotropin-Releasing Factor (CRF) Receptor Genes in Colorectal Cancer

doi: 10.3390/jcm10122680

Figure Lengend Snippet: Methylome datasets used for the bioinformatic analysis of CRFR1 and CRFR2 methylation.

Article Snippet: Thirty-four studies were found; of them, only those using Infinium Human Methylation 450K and EPIC BeadChips and providing adequate raw and clinical data were selected for further analysis.

Techniques: Methylation

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