Visualization Community | St. Jude Cloud

ChIP-SEQ landscape of primary medulloblastomas

St. Jude Children's Research Hospital

Jan 27, 2016

12.4K

ChIP Sequencing

ChIP-SEQ data (H3K27Ac, HLX, LHX2, and LMZ1A ChIP-SEQ tracks) for selected medulloblastoma patient samples are displayed. Samples are grouped into four medulloblastoma subtypes (WNT, SHH, Group 3, and Group 4). Different regions of the genome can be viewed by entering coordinates. Default view showing a Group 3 enhancer at the GLI1 gene locus.

Loading Visualization

runproteinpaint({
  host: "https://proteinpaint.stjude.org",
  holder: visualizationContainer[0],
  parseurl: true,
  block: true,
  nobox: 1,
  noheader: 1,
  genome: "hg19",
  position: "chr12:57799333-57920632",
  nativetracks: "RefGene",
  tracks: [
    {
      type: "bedj",
      name: "GROUP3-GROUP4 super enhancer",
      file: "files/hg19/MBSE2016/GROUP3-GROUP4_SE.bedj.gz",
    },
    {
      type: "bedj",
      name: "GROUP3 super enhancer",
      file: "files/hg19/MBSE2016/GROUP3_SE.bedj.gz",
    },
    {
      type: "bedj",
      name: "GROUP4 super enhancer",
      file: "files/hg19/MBSE2016/GROUP4_SE.bedj.gz",
    },
    {
      type: "bedj",
      name: "SHH-WNT super enhancer",
      file: "files/hg19/MBSE2016/SHH-WNT_SE.bedj.gz",
    },
    {
      type: "bedj",
      name: "SHH super enhancer",
      file: "files/hg19/MBSE2016/SHH_SE.bedj.gz",
    },
    {
      type: "bedj",
      name: "WNT super enhancer",
      file: "files/hg19/MBSE2016/WNT_SE.bedj.gz",
    },
    {
      type: "bedj",
      name: "CONSERVED super enhancer",
      file: "files/hg19/MBSE2016/CONSERVED_SE.bedj.gz",
    },
    {
      "type": "profilegenevalue",
      "name": "Group3 Subgroup",
      "tracks": [
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/D425_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "D425 H3K27Ac",
          "pcolor": "rgb(255,192,0)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/HD-MB03_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "HD-MB03 H3K27Ac",
          "pcolor": "rgb(255,192,0)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB-1M21_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB-1M21 H3K27Ac",
          "pcolor": "rgb(255,192,0)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB-4M23_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB-4M23 H3K27Ac",
          "pcolor": "rgb(255,192,0)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB-4M26_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB-4M26 H3K27Ac",
          "pcolor": "rgb(255,192,0)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB-4M77_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB-4M77 H3K27Ac",
          "pcolor": "rgb(255,192,0)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB18_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB18 H3K27Ac",
          "pcolor": "rgb(255,192,0)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB18_HLX_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB18 HLX",
          "pcolor": "rgb(0,192,55)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB18_LHX2_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB18 LHX2",
          "pcolor": "rgb(0,192,255)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB36_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB36 H3K27Ac",
          "pcolor": "rgb(255,192,0)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB90_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB90 H3K27Ac",
          "pcolor": "rgb(255,192,0)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB95_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB95 H3K27Ac",
          "pcolor": "rgb(255,192,0)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB9_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB9 H3K27Ac",
          "pcolor": "rgb(255,192,0)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB_4M26_HLX_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB_4M26 HLX",
          "pcolor": "rgb(0,192,55)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB_4M26_LHX2_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB_4M26 LHX2",
          "pcolor": "rgb(0,192,255)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MED8A_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MED8A H3K27Ac",
          "pcolor": "rgb(255,192,0)",
        },
      ],
    },
    {
      "type": "profilegenevalue",
      "name": "Group 4 Subgroup",
      "tracks": [
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/1M1_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "1M1 H3K27Ac",
          "pcolor": "rgb(79,98,40)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB110_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB110 H3K27Ac",
          "pcolor": "rgb(79,98,40)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB129_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB129 H3K27Ac",
          "pcolor": "rgb(79,98,40)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB129_LHX2_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB129 LHX2",
          "pcolor": "rgb(192,0,255)",

        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB129_LMX1A_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB129 LMX1A",
          "pcolor": "rgb(192,0,55)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB19_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB19 H3K27Ac",
          "pcolor": "rgb(79,98,40)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB26_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB26 H3K27Ac",
          "pcolor": "rgb(79,98,40)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB38_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB38 H3K27Ac",
          "pcolor": "rgb(79,98,40)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB40_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB40 H3K27Ac",
          "pcolor": "rgb(79,98,40)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB40_LHX2_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB40 LHX2",
          "pcolor": "rgb(192,0,255)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB40_LMX1A_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB40 LMX1A",
          "pcolor": "rgb(192,0,55)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB64_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB64 H3K27Ac",
          "pcolor": "rgb(79,98,40)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB7_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB7 H3K27Ac",
          "pcolor": "rgb(79,98,40)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB91_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB91 H3K27Ac",
          "pcolor": "rgb(79,98,40)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MBRep_T72_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MBRep_T72 H3K27Ac",
          "pcolor": "rgb(79,98,40)",
        },
      ],
    },
    {
      "type": "profilegenevalue",
      "name": "SHH Subgroup",
      "tracks": [
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB12_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB12 H3K27Ac",
          "pcolor": "rgb(192,0,0)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB206_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB206 H3K27Ac",
          "pcolor": "rgb(192,0,0)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB28_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB28 H3K27Ac",
          "pcolor": "rgb(192,0,0)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB35_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB35 H3K27Ac",
          "pcolor": "rgb(192,0,0)",

        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB37_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB37 H3K27Ac",
          "pcolor": "rgb(192,0,0)",
        },
      ],
    },
    {
      "type": "profilegenevalue",
      "name": "WNT Subgroup",
      "tracks": [
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB113_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB113 H3K27Ac",
          "pcolor": "rgb(0,69,134)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB176_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB176 H3K27Ac",
          "pcolor": "rgb(0,69,134)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB200_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB200 H3K27Ac",
          "pcolor": "rgb(0,69,134)",

        },
      ],
    },
  ],
});

Visualization Code

runproteinpaint({
  host: "https://proteinpaint.stjude.org",
  holder: visualizationContainer[0],
  parseurl: true,
  block: true,
  nobox: 1,
  noheader: 1,
  genome: "hg19",
  position: "chr12:57799333-57920632",
  nativetracks: "RefGene",
  tracks: [
    {
      type: "bedj",
      name: "GROUP3-GROUP4 super enhancer",
      file: "files/hg19/MBSE2016/GROUP3-GROUP4_SE.bedj.gz",
    },
    {
      type: "bedj",
      name: "GROUP3 super enhancer",
      file: "files/hg19/MBSE2016/GROUP3_SE.bedj.gz",
    },
    {
      type: "bedj",
      name: "GROUP4 super enhancer",
      file: "files/hg19/MBSE2016/GROUP4_SE.bedj.gz",
    },
    {
      type: "bedj",
      name: "SHH-WNT super enhancer",
      file: "files/hg19/MBSE2016/SHH-WNT_SE.bedj.gz",
    },
    {
      type: "bedj",
      name: "SHH super enhancer",
      file: "files/hg19/MBSE2016/SHH_SE.bedj.gz",
    },
    {
      type: "bedj",
      name: "WNT super enhancer",
      file: "files/hg19/MBSE2016/WNT_SE.bedj.gz",
    },
    {
      type: "bedj",
      name: "CONSERVED super enhancer",
      file: "files/hg19/MBSE2016/CONSERVED_SE.bedj.gz",
    },
    {
      "type": "profilegenevalue",
      "name": "Group3 Subgroup",
      "tracks": [
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/D425_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "D425 H3K27Ac",
          "pcolor": "rgb(255,192,0)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/HD-MB03_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "HD-MB03 H3K27Ac",
          "pcolor": "rgb(255,192,0)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB-1M21_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB-1M21 H3K27Ac",
          "pcolor": "rgb(255,192,0)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB-4M23_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB-4M23 H3K27Ac",
          "pcolor": "rgb(255,192,0)",
        },
        {
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          "file": "files/hg19/MBSE2016/MB-4M26_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB-4M26 H3K27Ac",
          "pcolor": "rgb(255,192,0)",
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        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB-4M77_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB-4M77 H3K27Ac",
          "pcolor": "rgb(255,192,0)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB18_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB18 H3K27Ac",
          "pcolor": "rgb(255,192,0)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB18_HLX_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB18 HLX",
          "pcolor": "rgb(0,192,55)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB18_LHX2_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB18 LHX2",
          "pcolor": "rgb(0,192,255)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB36_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB36 H3K27Ac",
          "pcolor": "rgb(255,192,0)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB90_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB90 H3K27Ac",
          "pcolor": "rgb(255,192,0)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB95_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB95 H3K27Ac",
          "pcolor": "rgb(255,192,0)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB9_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB9 H3K27Ac",
          "pcolor": "rgb(255,192,0)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB_4M26_HLX_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB_4M26 HLX",
          "pcolor": "rgb(0,192,55)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB_4M26_LHX2_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB_4M26 LHX2",
          "pcolor": "rgb(0,192,255)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MED8A_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MED8A H3K27Ac",
          "pcolor": "rgb(255,192,0)",
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      ],
    },
    {
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      "name": "Group 4 Subgroup",
      "tracks": [
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          "type": "bigwig",
          "file": "files/hg19/MBSE2016/1M1_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "1M1 H3K27Ac",
          "pcolor": "rgb(79,98,40)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB110_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB110 H3K27Ac",
          "pcolor": "rgb(79,98,40)",
        },
        {
          "type": "bigwig",
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          "height": 30,
          "name": "MB129 H3K27Ac",
          "pcolor": "rgb(79,98,40)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB129_LHX2_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB129 LHX2",
          "pcolor": "rgb(192,0,255)",

        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB129_LMX1A_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB129 LMX1A",
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        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB19_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB19 H3K27Ac",
          "pcolor": "rgb(79,98,40)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB26_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB26 H3K27Ac",
          "pcolor": "rgb(79,98,40)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB38_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB38 H3K27Ac",
          "pcolor": "rgb(79,98,40)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB40_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB40 H3K27Ac",
          "pcolor": "rgb(79,98,40)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB40_LHX2_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB40 LHX2",
          "pcolor": "rgb(192,0,255)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB40_LMX1A_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB40 LMX1A",
          "pcolor": "rgb(192,0,55)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB64_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB64 H3K27Ac",
          "pcolor": "rgb(79,98,40)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB7_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB7 H3K27Ac",
          "pcolor": "rgb(79,98,40)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB91_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB91 H3K27Ac",
          "pcolor": "rgb(79,98,40)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MBRep_T72_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MBRep_T72 H3K27Ac",
          "pcolor": "rgb(79,98,40)",
        },
      ],
    },
    {
      "type": "profilegenevalue",
      "name": "SHH Subgroup",
      "tracks": [
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB12_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB12 H3K27Ac",
          "pcolor": "rgb(192,0,0)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB206_H3K27Ac_treat_afterfiting_all.bw",
          "height": 30,
          "name": "MB206 H3K27Ac",
          "pcolor": "rgb(192,0,0)",
        },
        {
          "type": "bigwig",
          "file": "files/hg19/MBSE2016/MB28_H3K27Ac_treat_afterfiting_all.bw",
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ChIP-SEQ landscape of primary medulloblastomas

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