Novel region discovery method for Infinium 450K DNA methylation data reveals changes associated with aging in muscle and neuronal pathways
Version of Record online: 22 OCT 2013
© 2013 The Authors. Aging Cell published by the Anatomical Society and John Wiley & Sons Ltd.
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Volume 13, Issue 1, pages 142–155, February 2014
How to Cite
Ong, M.-L. and Holbrook, J. D. (2014), Novel region discovery method for Infinium 450K DNA methylation data reveals changes associated with aging in muscle and neuronal pathways. Aging Cell, 13: 142–155. doi: 10.1111/acel.12159
- Issue online: 16 JAN 2014
- Version of Record online: 22 OCT 2013
- Accepted manuscript online: 23 SEP 2013 03:45AM EST
- Manuscript Accepted: 31 AUG 2013
Fig. S1 CpGs typed on Infinium 450K array are irregularly spaced in the genome: Frequency distribution of distance (bp) between neighbouring CpGs on the Infinium 450K array. The inset shows a zoomed-in region of distances less than 5000 bp, where the majority of CpGs reside.
Fig. S2 Correlation of CpG methylation levels of probes within close distances is discernible of the Infinium 450K array: Pearson correlation of pairwise Infinium 450K measured methylation levels (y-axis) with distance (bp) (x-axis). The inset shows a zoomed-in region of distances < 2500 bp, where the correlation ranges from approximately 0.9 to 0.1.
Fig. S3 Correlation of CpG methylation levels with distance for different age groups: a) Pearson correlation of pairwise Infinium 450K measured methylation levels (y-axis) with distance (bp) (x-axis). b) The figure shows a zoomed-in region of distance < 250 bp.
Fig. S4 Relationship between number of significant DMRs identified and a) sample size or b) age difference in sample set.
Fig. S5 Relationship between number of significant VMRs identified and a) sample size or b) median subject age in sample set.
Fig. S6 Heat map of CpG island enrichment results. Genomic regions of varying proximity to CpG islands are indicated on the x-axis and region lists on the y-axis. Cells are coloured for P-value of enrichment.
Table S1 Lists of significant DMRs and VMRs.
Table S2 Gene ontology categories for DMR and VMR lists with P < 10−4 and FDR < 5%
Table S3 Overall enrichment of DMR and VMR lists for neurotransmitter genes.
Table S4 Overlap of DMRs and VMRs with DNase I hypersensitivity hot spots of three other blood cell types.
Table S5 Coverage (no of probes on the array that can be grouped into regions by distance) as a function of the distance threshold.
Table S6 Comparison of power achieved using single probe and region analysis on the extreme data set.
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