INSTRUCTIONS

■ Tracks

  • 1. Reference sequence
    • Reference sequence: Human genome hg19/GRCh37 sequence.
  • 2. IMM: 3 cell-types
    • CpG_CD4T, CpG_Mono, CpG_Neu: Information of each CpG site.
    • CpG_CD4T_avg, CpG_Mono_avg, CpG_Neu_avg: Average methylation levels of each CpG site.
    • CpG_CD4T_sd, CpG_Mono_sd, CpG_Neu_sd: SD (standard deviations) for the methylation levels of each CpG site.
    • CpG_CD4T_RI, CpG_Mono_RI, CpG_Neu_RI: RI (reference interval) for the methylation levels of each CpG site.
    • FPKM_CD4T, FPKM_Mono, FPKM_Neu: FPKM (fragments per kilobase of exon per million fragments mapped) values of each transcript.
    • SNV_CD4T, SNV_Mono, SNV_Neu: SNV (single nucleotide variant, minor allele count > 1 and call rate ≥ 50%).
  • 3. IMM: 8 cell-populations
    • All tracks: Average methylation levels of each CpG site of each cell-population obtained from WGBS of 20 individuals.
  • 4. IMM: QTL
    • eQTL: Results of eQTL analysis (only the results with FDR ≤ 0.05 are presented).
    • eQTM: Results of eQTM analysis (only the results with FDR ≤ 0.05 are presented).
    • mQTL: Results of mQTL analysis (only the results with FDR ≤ 0.05 are presented).
  • 5. Others
    • RepeatMasker: Repetitive elements from UCSC genome browser.
    • CpGIslandsExt: CpG Island locations obtained from UCSC genome browser.
    • HM450: probe information of Illumina Infinium HumanMethylation450 Array BeadChips.
    • genecode_v19: Information of genes obtained from GENCODE version 19.
    • genecode_v19_trs: Information of transcripts obtained from GENCODE version 19.

■ How to Use

Click “Genome Browser” tab in the navigation menu, and search a gene or region of your interest by following the instructions below.


■ Search methods

  • Search by Gene Symbol
    • Enter any gene symbol in the box and press the Go button.

    • Ex; Enter the “LYZ” and press the button. Choose gencode_v19 from the pop-up menu and press the Go button.

    • You can find differencially methylated CpG sites among cell types at the LYZ gene region.

  • Search by Genomic Region
    • Enter any genomic position or region in the box and press the Go button.
    • Ex; Select “chr1” from select box and enter the “206906382” in the box, and then press the Go button.

    • You can find CD4+ T cells specific demethylation CpG site at the intergenic region between IL10 and IL19.

■ Details of CpG track

  • Click the bar in the CpG tracks. You can see distribution of methylation levels of each CpG site in the pop-up window.


  • Details of the FPKM track
    • Click the bar in the FPKM tracks. You can see distribution of expression levels of each gene in the pop-up window
      • ex8.png

      ex9.png

  • Details of the SNV track
    • Click the bar in the SNV track. You can see detail information of each SNV in the pop-up window.
      • ex10.png ex11.png

  • Terms
    • Cell Type; Name of each cell type (Mono; monocytes, CD4T; CD4+ T cells, Neu; neutrophils)
    • Mlf_high,Mlf_mid, and Mlf_low; Frequency of 102 individuals in each category. Mlf_high means more than 66% methylation, Mlf_mid means between 34-66% methylation, and Mlf_low means less than 34% CpG methylation.
    • Allele_frequency; Proportion of alternative allele among the total alleles for the subjects in the SNV tracks.
　　　　　　
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