How to Use

■ Click “Genome Browser” tab and Search a gene or region of your interest by following the instructions below.


■ Tracks

  • Reference sequence; Human genome hg19/GRCh37 sequence.
  • 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.
  • IMM_CpG_CD4T, IMM_CpG_Mono, IMM_CpG_Neu; Information of each CpG site (for more details, see Details of CpG track).
  • IMM_CpG_CD4T_avg, IMM_CpG_Mono_avg, IMM_CpG_Neu_avg; Average methylation levels of each CpG site.
  • IMM_CpG_CD4T_sd, IMM_CpG_Mono_sd, IMM_CpG_Neu_sd; SD (standard deviations) for the methylation levels of each CpG site.
  • IMM_CpG_CD4T_RI, IMM_CpG_Mono_RI, IMM_CpG_Neu_RI; RI (reference interval) for the methylation levels of each CpG site.
  • IMM_FPKM_CD4T, IMM_FPKM_Mono, IMM_FPKM_Neu; FPKM (fragments per kilobase of exon per million fragments mapped) values of each transcript (for more details, see Details of FPKM track).
  • IMM_SNV; SNV (single nucleotide variant, minor allele frequency > 5% and reported in dbSNP138). For more details, see Details of SNV track.

■ 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 monocyte specific demethylations 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 “206957874” 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 blue 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 blue bar in the FPKM tracks. You can see distribution of expression levels of each gene in the pop-up windo
    • ex8.png ex9.png

  • Details of the SNV track
    • Click the yellow brown 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.
    • Immfq; Proportion of alternative allele among the total alleles for the subjects in the SNV tracks.
      
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