HF-VHF帯における生体等価ファントムを用いた電磁波と人体相互作用の検証

研究科: 千葉大学大学院工学研究科学位:千大院工博甲第工185号博士(工学)千葉大

Additional file 7: Table S6. of DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas

Three-way comparison of the test tumour set of pilocytic and diffuse astrocytomas with normal brain control tissue. 993 CpG probes are shown where the difference between the average beta values of pilocytic and diffuse astrocytomas, or between either of these and the control samples is equal to or greater than 0.3 (δβ ≥ 0.3, Benjamini-Hochberg corrected p-value <0.05), assessed by MethLAB. Illumina annotation is included. (XLSX 436 kb

Additional file 21: Table S20. of DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas

Differentially methylated CpG sites in infratentorial pilocytic astrocytomas, supratentorial astrocytomas and diffuse astrocytomas. 1_ MethLAB analysis identified 676 CpG sites that are significantly differentially methylated in infratentorial pilocytic, supratentorial pilocytic and diffuse astrocytomas (Benjamini-Hochberg corrected p-value <0.05). 2_ The 72 differentially methylated CpG sites in supratentorial and infratentorial pilocytic astrocytomas. 3_ The 393 differentially methylated CpG sites for infratentorial pilocytic astrocytomas and diffuse astrocytomas (averaged beta values with δβ ≥ 0.3, Benjamini-Hochberg corrected p-value <0.05). 4_ Genes that show differentially methylated CpG sites and expression between supratentorial and infratentorial pilocytic astrocytomas (genes with fold change ≥ 2 highlighted in grey). (XLSX 406 kb

Additional file 10: Table S9. of DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas

Comparison of pilocytic astrocytomas with diffuse astrocytomas in the test tumour set. 315 CpG sites are shown where δβ ≥ 0.3 (Benjamini-Hochberg corrected p-value <0.05), assessed by MethLAB. Illumina annotation is included. Rows highlighted in grey (42/315 CpG sites) were absent in the 993 differentially methylated CpG sites between tumours and normal brain control. Ordered by chromosomal location. (XLSX 205 kb

Additional file 12: Table S11. of DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas

Normalised log2 expression values for the genes associated with the 315 CpG sites. The δβ values between the pilocytic and diffuse astrocytoma groups were obtained from the grouped averaged beta values. Genes with a differential gene expression ≥2 fold are highlighted in grey. Sorted alphabetically by gene symbol. (XLSX 370 kb

Additional file 18: Table S17. of DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas

Ingenuity Pathway Analysis (IPA) of genes associated with differentially methylated sites in infratentorial pilocytic astrocytomas and normal cerebellum. IPA analysis of the top 20 significant biological and disease categories including their functional annotation (p-value <0.05) identified for 161 genes that had ≤2 fold change in gene expression and δβ ≥ 0.3, sorted by p-value. (XLSX 71 kb

Additional file 1: Table S1. of DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas

Study tumour set, validation tumour set and controls. Clinical features of patients, tumour pathology and genetic changes are shown. Samples that were included in the whole genome sequencing (WGS) study of the Pediatric Cancer Genome Project (PCGP) are noted together with the original patient numbers [Zhang et al, Nature Genetics 45(6):602-614, 2013]. (XLSX 406 kb

Additional file 3: of DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas

Supplementary Methods; Legends to Supplementary Tables; Supplementary Figures. (PDF 1904 kb

Additional file 20: Table S19. of DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas

Differentially methylated CpG sites identified between diffuse astrocytomas and cerebral cortex controls. 1_ MethLAB analysis identified 90,249 CpG sites that are significantly differentially methylated in supratentorial pilocytic astrocytomas, diffuse astrocytomas, glial component of the cerebral cortex, neuronal component of the cerebral cortex, adult cerebral cortex and foetal cerebral cortex (Benjamini-Hochberg corrected p-value <0.05). The adult cerebral cortex controls (including the glial and neuronal components) were taken from [Guintivano et al, Epigenetics 8:290-302, 2013]. The number of differentially methylated sites (averaged beta values with a difference of δβ ≥ 0.3, Benjamini-Hochberg corrected p-value <0.05) identified in tumour and all controls was 58 CpG sites for the diffuse astrocytomas. 2_ CpG sites hypermethylated and 3_ hypomethylated in diffuse astrocytomas compared to controls. 4_ Expression analysis for the genes that show differentially methylated CpG sites. Highlighted genes show ≤ 2 fold change in expression compared to controls. (XLSX 37720 kb

Additional file 13: Table S12. of DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas

Comparison of methylation and expression for genes associated with 315 differentially methylated sites in pilocytic and diffuse astrocytomas. Correlation coefficients are shown for differentially methylated CpG sites that show a difference of ≥2-fold in expression of the associated gene. Expression probes were only assessed if they were located within the mRNA transcript. A) CpG sites located within the promoter of the gene. B) CpG sites located within the gene body, 3’UTR and intergenic regions. As the CpG is not within a promoter, correlation was also calculated for a CpG site within the promoter (where possible within the TSS200; brown panel). For each correlation p-values and Benjamini-Hochberg corrected p-values are shown. The table is ordered by FDR-corrected p-values (sites with a p-value <0.05 are shown in blue). Positive correlation is highlighted in yellow. Up-regulated genes in diffuse astrocytomas are highlighted in green. When the expression probe was located in an exon, the probe for the full transcript was used for the correlation (indicated by the asterisk). (XLSX 85 kb