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INFINIUM Inc microarray data

Genomic alterations, expression, and epigenetic regulation of SAPCD2 in gastrointestinal tumors. ( A ) The landscape of the copy number amplification and mutation frequency of SAPCD2 gene in various tumor types. ( B ) Potential mutations sites across the SAPCD2 protein in various cancers. Green dots, missense mutations; Black dots, truncating mutations; Brown dots, in-frame mutations. The hotspot mutation (E234K) is observed in the conserved Suppressor_APC domain. ( C ) The CNV percentage in each GI tumor. ( D ) The correlation between CNV and RNA-seq derived SAPCD2 gene expression in digestive tumors. ( E ) The differences of the patients’ survival between the CNV group and the wild type group in digestive tumors. ( F ) The diagram of the genomic structure of human SAPCD2 gene. The green box indicates the CpG island locus; the Orange boxes indicate the 6 exons’ locus; the red boxes indicate the positions of the 8 probes for evaluating the DNA methylation status; the grey arrow indicates the transcription direction of SAPCD2 gene whose cDNA is 8431 base pairs long. The width of each box indicates its relative length, and numbers within the square brackets indicates the start and end sites respectively. The 8 probes in this study are: cg15733507, cg21241219, cg21066537, cg15785720, cg03180426, cg01448891, cg14607755, cg14156314. ( G ) The summarized view of the relationship between the RNA-seq derived SAPCD2 gene expression and DNA methylation at 8 probes sites in TCGA-PAAD cohort. Each probe (Infinium Human Methylation 450 microarray data) was indicated on the left side, and the numbers on the right side indicated the correlation <t>coefficient</t> or P value. *p<0.05, **p<0.01, ***p<0.001. ( H ) The detailed view of the relationship between of SAPCD2 gene expression and DNA methylation at 8 probes sites in TCGA-PAAD cohort. The methylation level differed in SAPCD2 gene high and low expression group at 3 probe sites: cg21241219*, cg03180426 ***, cg14156314 ***.

Microarray Data, supplied by INFINIUM Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/microarray+expression+and+methylation+probe/microarray/pmc11873019-136-23-2
Average 90 stars, based on 1 article reviews

microarray data - by Bioz Stars, 2026-09

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1) Product Images from "Comprehensive Bioinformatics Analyses and Experimental Validation of the Cell Cycle Related Protein SAPCD2 as a New Biomarker and Potential Therapeutic Target in Pancreatic Cancer"

Article Title: Comprehensive Bioinformatics Analyses and Experimental Validation of the Cell Cycle Related Protein SAPCD2 as a New Biomarker and Potential Therapeutic Target in Pancreatic Cancer

Journal: Journal of Inflammation Research

doi: 10.2147/JIR.S501850

Figure Legend Snippet: Genomic alterations, expression, and epigenetic regulation of SAPCD2 in gastrointestinal tumors. ( A ) The landscape of the copy number amplification and mutation frequency of SAPCD2 gene in various tumor types. ( B ) Potential mutations sites across the SAPCD2 protein in various cancers. Green dots, missense mutations; Black dots, truncating mutations; Brown dots, in-frame mutations. The hotspot mutation (E234K) is observed in the conserved Suppressor_APC domain. ( C ) The CNV percentage in each GI tumor. ( D ) The correlation between CNV and RNA-seq derived SAPCD2 gene expression in digestive tumors. ( E ) The differences of the patients’ survival between the CNV group and the wild type group in digestive tumors. ( F ) The diagram of the genomic structure of human SAPCD2 gene. The green box indicates the CpG island locus; the Orange boxes indicate the 6 exons’ locus; the red boxes indicate the positions of the 8 probes for evaluating the DNA methylation status; the grey arrow indicates the transcription direction of SAPCD2 gene whose cDNA is 8431 base pairs long. The width of each box indicates its relative length, and numbers within the square brackets indicates the start and end sites respectively. The 8 probes in this study are: cg15733507, cg21241219, cg21066537, cg15785720, cg03180426, cg01448891, cg14607755, cg14156314. ( G ) The summarized view of the relationship between the RNA-seq derived SAPCD2 gene expression and DNA methylation at 8 probes sites in TCGA-PAAD cohort. Each probe (Infinium Human Methylation 450 microarray data) was indicated on the left side, and the numbers on the right side indicated the correlation coefficient or P value. *p<0.05, **p<0.01, ***p<0.001. ( H ) The detailed view of the relationship between of SAPCD2 gene expression and DNA methylation at 8 probes sites in TCGA-PAAD cohort. The methylation level differed in SAPCD2 gene high and low expression group at 3 probe sites: cg21241219*, cg03180426 ***, cg14156314 ***.

Techniques Used: Expressing, Amplification, Mutagenesis, RNA Sequencing, Derivative Assay, Gene Expression, DNA Methylation Assay, Methylation, Microarray

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We collected published datasets of human blood samples for gene expression, DNA methylation, and single-cell transcriptomic data. The analysis aimed to study the relation between the expression and DNA methylation of retrotransposons (RTEs) versus chronological and biological aging in large human cohorts. The single-cell transcriptomic datasets were employed for cell type-specific analysis of RTEs in peripheral blood mononuclear cell (PBMC) to identify the relation between RTE expression and aging events for annotated cell types within old versus young PBMC samples.

Journal: eLife

Article Title: Expression of most retrotransposons in human blood correlates with biological aging

doi: 10.7554/eLife.96575

Figure Lengend Snippet: We collected published datasets of human blood samples for gene expression, DNA methylation, and single-cell transcriptomic data. The analysis aimed to study the relation between the expression and DNA methylation of retrotransposons (RTEs) versus chronological and biological aging in large human cohorts. The single-cell transcriptomic datasets were employed for cell type-specific analysis of RTEs in peripheral blood mononuclear cell (PBMC) to identify the relation between RTE expression and aging events for annotated cell types within old versus young PBMC samples.

Article Snippet: By overlapping Illumina microarray expression and methylation probe locations to RTE locations in RepeatMasker , we were able to identify a sufficient number of probes to calculate the expression and methylation levels of RTE classes and families.

Techniques: Gene Expression, DNA Methylation Assay, Expressing

(a, b), Methylation levels of RTE classes inversely correlated with chronological age in monocyte (Multi-Ethnic Study of Atherosclerosis, MESA) and whole blood (WB) (BSGS, SATSA, and GMPWAR) samples. Satellite DNA was included as a control group. ( c ), Methylation levels versus low (first quartile), medium (second and third quartile), and high (fourth quartile) expressions of RTE classes in monocytes (MESA). Wilcoxon test; ns: not significant. ( d ), Correlation matrix for RTE expressions and methylation levels, and chronological age. *p≤0.05, **p≤0.01, ***p≤0.001, ****p≤0.0001, Pearson’s correlation. MESA, n=1202; BSGS, n=614; GMPWAR, n=656; SATSA, n=1072.

Journal: eLife

Article Title: Expression of most retrotransposons in human blood correlates with biological aging

doi: 10.7554/eLife.96575

Figure Lengend Snippet: (a, b), Methylation levels of RTE classes inversely correlated with chronological age in monocyte (Multi-Ethnic Study of Atherosclerosis, MESA) and whole blood (WB) (BSGS, SATSA, and GMPWAR) samples. Satellite DNA was included as a control group. ( c ), Methylation levels versus low (first quartile), medium (second and third quartile), and high (fourth quartile) expressions of RTE classes in monocytes (MESA). Wilcoxon test; ns: not significant. ( d ), Correlation matrix for RTE expressions and methylation levels, and chronological age. *p≤0.05, **p≤0.01, ***p≤0.001, ****p≤0.0001, Pearson’s correlation. MESA, n=1202; BSGS, n=614; GMPWAR, n=656; SATSA, n=1072.

Techniques: Methylation, Control

(a, b), Methylation levels of long terminal repeats (LTR) and LINE/SINE families negatively correlate with chronological age in monocytes (MESA) and the WB (BSGS, SATSA, and GMPWAR). **p≤0.01, ***p≤0.001, Wilcoxon test.

Journal: eLife

Article Title: Expression of most retrotransposons in human blood correlates with biological aging

doi: 10.7554/eLife.96575

Figure Lengend Snippet: (a, b), Methylation levels of long terminal repeats (LTR) and LINE/SINE families negatively correlate with chronological age in monocytes (MESA) and the WB (BSGS, SATSA, and GMPWAR). **p≤0.01, ***p≤0.001, Wilcoxon test.

Techniques: Methylation

While LINE families, MIR, and long terminal repeats (LTR) families except ERVK show lower levels of methylation in higher expression groups, this pattern is not seen in Alu, CR1, and ERVl. *p≤0.05, **p≤0.01, ***p≤0.001, ****p≤0.0001, ns: not significant, Wilcoxon test.

Journal: eLife

Article Title: Expression of most retrotransposons in human blood correlates with biological aging

doi: 10.7554/eLife.96575

Figure Lengend Snippet: While LINE families, MIR, and long terminal repeats (LTR) families except ERVK show lower levels of methylation in higher expression groups, this pattern is not seen in Alu, CR1, and ERVl. *p≤0.05, **p≤0.01, ***p≤0.001, ****p≤0.0001, ns: not significant, Wilcoxon test.

Techniques: Methylation, Expressing

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1) Product Images from "Comprehensive Bioinformatics Analyses and Experimental Validation of the Cell Cycle Related Protein SAPCD2 as a New Biomarker and Potential Therapeutic Target in Pancreatic Cancer"

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