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Identification of DNA methylation changes associated with human gastric cancer

Jung-Hoon Park1, Jinah Park3, Jung Kyoon Choi45, Jaemyun Lyu1, Min-Gyun Bae1, Young-Gun Lee1, Jae-Bum Bae1, Dong Yoon Park1, Han-Kwang Yang3, Tae-You Kim3* and Young-Joon Kim12*

Author Affiliations

1 Department of Biochemistry, College of Life Science and Technology, Yonsei University, Seoul, Korea

2 Department of Integrated Omics for Biomedical Science, WCU Program of Graduate School, Yonsei University, Seoul, Korea

3 Cancer Research Institute, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea

4 Department of Bio and Brain Engineering, KAIST, Daejeon, Korea

5 Computational and Systems Biology, Genome Institute of Singapore, Singapore, Singapore

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BMC Medical Genomics 2011, 4:82  doi:10.1186/1755-8794-4-82

Published: 2 December 2011

Additional files

Additional file 1:

Supplementary Tables 1. Supplementary Table 1: Primers for pyrosequencing, MSP and MIRA-qPCR. Supplementary Table 2: Number of uniquely matched reads (U0, U1, and U2 from ELAND alignment results) in each experiment. Supplementary Table 3: Number of covered genomic CpG sites and total CpG counts in our methylome. Supplementary Table 5: Comparison of 5', intragenic and intergenic CGIs. Supplementary Table 8: Functional annotation clustering of genes with hypermethylated 5'CGIs in metastatic lymph nodes.

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Additional file 2:

Supplementary Figures. Supplementary Figure 1: Sensitivity of the MIRA technique. Supplementary Figure 2: The distribution of MESs from MIRA-seq, input and randomized methylome of normal. Supplementary Figure 3: Goodness of fit was tested for two basic normalized MESs (MESt and MESl), two background normalized MESs (MESt-MESbg and MESl-MESbg), and raw readcounts against the Poisson and Gaussian model. Supplementary Figure 4: Average MES pattern of human promoters which were subgrouped into high, intermediate, and low CpG density promoters (HCP, ICP, and LCP, respectively). Supplementary Figure 5: Chromosome-wide average MESs for normal (black circle) and cancerous (red circle) tissue. Supplementary Figure 6: Chromosomal distribution of the average MES (black (normal) and red (cancer) curve corresponding to the left axis) and the average CpG observed/expected ratio (gray shade corresponding to the left axis) in 1 Mb sliding windows. Supplementary Figure 7: Average MES pattern of subgrouped CGIs (5'CGIs, intergenic CGIs and intergenic CGIs). Supplementary Figure 8: Plots of several genes with 5'CGIs hypermethylation. Supplementary Figure 9: MDM2 methylation level of normal and cancerous tissue in three individual samples by pyrosequencing. Supplementary Figure 10: Amplification ratio of several genes (DYRK2, IFNG, IL26, MDM1, and MDM2) within chromosome 12q14 LRES region by real-time qPCR. Supplementary Figure 11: Amplification ratio of specific locus in an upstream region of MDM2 by real-time qPCR.

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Additional file 3:

Supplementary Tables 2. Supplementary Table 4, 6, 7. Supplementary Table 4: Promoter class according to CpG density. Supplementary Table 6: The genes with hypermethylation patterns and low expression levels. Supplementary Table 7: The genes with hypomethylation patterns and high expression levels.

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