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Sarcoma
Volume 2015, Article ID 412068, 14 pages
http://dx.doi.org/10.1155/2015/412068
Research Article

Genomic, Epigenomic, and Transcriptomic Profiling towards Identifying Omics Features and Specific Biomarkers That Distinguish Uterine Leiomyosarcoma and Leiomyoma at Molecular Levels

1Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
2Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
3Department of Systems BioMedicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
4Department of Health Nutrition, Faculty of Health Science, Kio University, 4-2-4 Umami-naka, Koryo-cho, Kitakatsuragi-gun 635-0832, Japan
5Department of Obstetrics and Gynecology, Faculty of Medicine, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima 890-0075, Japan

Received 21 September 2015; Accepted 24 November 2015

Academic Editor: Eugenie S. Kleinerman

Copyright © 2015 Tomoko Miyata et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Supplementary Material

Figure S1: Venn diagrams for the probes detecting differential gene expression in LM and LMS samples compared to the average of NM samples.

Figure S2: A standard curve for the COBRA assay for LINE1 repetitive sequences.

Figure S3: Ontology terms in the InterPro category detected to be enriched among the differentially methylated regions in LMS (compared to NM) in the GREAT annotation.

Figure S4: DNA methylation profiles of NM, LM, and LMS samples visualized using Integrative Genomic Viewer (https://www.broadinstitute.org/igv/).

Figure S5: Methylation by expression plots of LMS compared to NM.

Table S1: Genomic sizes and ratios of the chromosomal abnormalities detected by SNP array analysis.

Table S2: Filter conditions used for the selection of candidate expression markers.

Table S3: Full list of candidate expression markers selected using filter conditions shown in Table S3.

Table S4: Full results of DAVID’s gene ontology analysis for differentially expressed genes in each of LM and LMS samples compared to the average of NM samples.

Table S5: List of 7110 genes hosting differentially methylated regions in LMS compared to NM detected by IMA.

Table S6: Full results of GREAT annotation for differentially methylated regions in LMS compared to NM.

Table S7: β values and Z-scores of 133 CpG probes in the TSS200 regions of the 37 PcG target gene loci and of 47 CpG probes in the TSS200 regions of the 15 protocadherin gene loci hypermethylated (Δβ > 0.2) in LMS compared to NM.

  1. Supplementary Figures
  2. Supplementary Table 1
  3. Supplementary Table 2
  4. Supplementary Table 3
  5. Supplementary Table 4
  6. Supplementary Table 5
  7. Supplementary Table 6
  8. Supplementary Table 7