Visualization Community | St. Jude Cloud

Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors

St. Jude Children's Research Hospital

50 4

Aug 30, 2017

PMID 28854174

10.6K

RNA Sequencing

ChIP Sequencing

Summary view of HMM states for patient derived xenografts of pediatric solid tumors. Mousing over each colored bars reveals the HMM state. The FPKM expression value of the first gene in the viewing window is displayed as a bar plot on the right.

Loading Visualization

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              "sampleID": "MAST 22",
              "name": "OS"
            },
            {
              "type": "bedj",
              "file": "files/hg19/rhb-mast-nature2017/mast3.gz",
              "stackheight": 20,
              "stackspace": 1,
              "onerow": 1,
              "sampleID": "MAST 3",
              "name": "NB"
            }
          ]
        }
      ]
    },
    "show_browser": 1,
    "hide_navigation": 1
  }
});

Visualization Code

runproteinpaint({
  "host": "https://proteinpaint.stjude.org",
  "holder": visualizationContainer[0],
  "noheader": true,
  "studyview": {
    "genome": "hg19",
    "name": "MAST epigenome, expression, and proteome",
    "assays": [
      "BRD4",
      "CTCF",
      "H3K27Ac",
      "H3K27me3",
      "H3K36me3",
      "H3K4me1",
      "H3K4me2",
      "H3K4me3",
      "H3K9-14Ac",
      "H3K9me2",
      "H3K9me3",
      "INPUT",
      "RNAPolII"
    ],
    "BRD4": {
      "config": {
        "pcolor": "255,0,255",
        "type": "bigwig",
        "height": "10"
      },
      "OS": {
        "OS": {
          "pcolor": "rgb(255,0,255)",
          "pcolor2": "rgb(255,0,255)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast22-BRD4.bw",
          "height": 15
        }
      },
      "ERMS": {
        "ERMS": {
          "pcolor": "rgb(255,0,255)",
          "pcolor2": "rgb(255,0,255)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast39-BRD4.bw",
          "height": 15
        }
      },
      "NB": {
        "NB": {
          "pcolor": "rgb(255,0,255)",
          "pcolor2": "rgb(255,0,255)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast3-BRD4.bw",
          "height": 15
        }
      },
      "ARMS": {
        "ARMS": {
          "pcolor": "rgb(255,0,255)",
          "pcolor2": "rgb(255,0,255)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast60-BRD4.bw",
          "height": 15
        }
      }
    },
    "CTCF": {
      "config": {
        "pcolor": "0,153,153",
        "type": "bigwig",
        "height": "10"
      },
      "OS": {
        "OS": {
          "pcolor": "rgb(0,153,153)",
          "pcolor2": "rgb(0,153,153)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast22-CTCF.bw",
          "height": 15
        }
      },
      "ERMS": {
        "ERMS": {
          "pcolor": "rgb(0,153,153)",
          "pcolor2": "rgb(0,153,153)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast39-CTCF.bw",
          "height": 15
        }
      },
      "NB": {
        "NB": {
          "pcolor": "rgb(0,153,153)",
          "pcolor2": "rgb(0,153,153)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast3-CTCF.bw",
          "height": 15
        }
      },
      "ARMS": {
        "ARMS": {
          "pcolor": "rgb(0,153,153)",
          "pcolor2": "rgb(0,153,153)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast60-CTCF.bw",
          "height": 15
        }
      }
    },
    "H3K27Ac": {
      "config": {
        "pcolor": "0,51,255",
        "type": "bigwig",
        "height": "10"
      },
      "OS": {
        "OS": {
          "pcolor": "rgb(0,51,255)",
          "pcolor2": "rgb(0,51,255)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast22-H3K27Ac.bw",
          "height": 15
        }
      },
      "ERMS": {
        "ERMS": {
          "pcolor": "rgb(0,51,255)",
          "pcolor2": "rgb(0,51,255)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast39-H3K27Ac.bw",
          "height": 15
        }
      },
      "NB": {
        "NB": {
          "pcolor": "rgb(0,51,255)",
          "pcolor2": "rgb(0,51,255)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast3-H3K27Ac.bw",
          "height": 15
        }
      },
      "ARMS": {
        "ARMS": {
          "pcolor": "rgb(0,51,255)",
          "pcolor2": "rgb(0,51,255)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast60-H3K27Ac.bw",
          "height": 15
        }
      }
    },
    "H3K27me3": {
      "config": {
        "pcolor": "102,102,0",
        "type": "bigwig",
        "height": "10"
      },
      "OS": {
        "OS": {
          "pcolor": "rgb(102,102,0)",
          "pcolor2": "rgb(102,102,0)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast22-H3K27me3.bw",
          "height": 15
        }
      },
      "ERMS": {
        "ERMS": {
          "pcolor": "rgb(102,102,0)",
          "pcolor2": "rgb(102,102,0)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast39-H3K27me3.bw",
          "height": 15
        }
      },
      "NB": {
        "NB": {
          "pcolor": "rgb(102,102,0)",
          "pcolor2": "rgb(102,102,0)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast3-H3K27me3.bw",
          "height": 15
        }
      },
      "ARMS": {
        "ARMS": {
          "pcolor": "rgb(102,102,0)",
          "pcolor2": "rgb(102,102,0)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast60-H3K27me3.bw",
          "height": 15
        }
      }
    },
    "H3K36me3": {
      "config": {
        "pcolor": "0,255,0",
        "type": "bigwig",
        "height": "10"
      },
      "OS": {
        "OS": {
          "pcolor": "rgb(0,255,0)",
          "pcolor2": "rgb(0,255,0)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast22-H3K36me3.bw",
          "height": 15
        }
      },
      "ERMS": {
        "ERMS": {
          "pcolor": "rgb(0,255,0)",
          "pcolor2": "rgb(0,255,0)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast39-H3K36me3.bw",
          "height": 15
        }
      },
      "NB": {
        "NB": {
          "pcolor": "rgb(0,255,0)",
          "pcolor2": "rgb(0,255,0)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast3-H3K36me3.bw",
          "height": 15
        }
      },
      "ARMS": {
        "ARMS": {
          "pcolor": "rgb(0,255,0)",
          "pcolor2": "rgb(0,255,0)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast60-H3K36me3.bw",
          "height": 15
        }
      }
    },
    "H3K4me1": {
      "config": {
        "pcolor": "102,0,204",
        "type": "bigwig",
        "height": "10"
      },
      "OS": {
        "OS": {
          "pcolor": "rgb(102,0,204)",
          "pcolor2": "rgb(102,0,204)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast22-H3K4me1.bw",
          "height": 15
        }
      },
      "ERMS": {
        "ERMS": {
          "pcolor": "rgb(102,0,204)",
          "pcolor2": "rgb(102,0,204)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast39-H3K4me1.bw",
          "height": 15
        }
      },
      "NB": {
        "NB": {
          "pcolor": "rgb(102,0,204)",
          "pcolor2": "rgb(102,0,204)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast3-H3K4me1.bw",
          "height": 15
        }
      },
      "ARMS": {
        "ARMS": {
          "pcolor": "rgb(102,0,204)",
          "pcolor2": "rgb(102,0,204)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast60-H3K4me1.bw",
          "height": 15
        }
      }
    },
    "H3K4me2": {
      "config": {
        "pcolor": "153,0,153",
        "type": "bigwig",
        "height": "10"
      },
      "OS": {
        "OS": {
          "pcolor": "rgb(153,0,153)",
          "pcolor2": "rgb(153,0,153)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast22-H3K4me2.bw",
          "height": 15
        }
      },
      "ERMS": {
        "ERMS": {
          "pcolor": "rgb(153,0,153)",
          "pcolor2": "rgb(153,0,153)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast39-H3K4me2.bw",
          "height": 15
        }
      },
      "NB": {
        "NB": {
          "pcolor": "rgb(153,0,153)",
          "pcolor2": "rgb(153,0,153)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast3-H3K4me2.bw",
          "height": 15
        }
      },
      "ARMS": {
        "ARMS": {
          "pcolor": "rgb(153,0,153)",
          "pcolor2": "rgb(153,0,153)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast60-H3K4me2.bw",
          "height": 15
        }
      }
    },
    "H3K4me3": {
      "config": {
        "pcolor": "255,0,255",
        "type": "bigwig",
        "height": "10"
      },
      "OS": {
        "OS": {
          "pcolor": "rgb(255,0,255)",
          "pcolor2": "rgb(255,0,255)",
          "scale": {
            "max": 200,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast22-H3K4me3.bw",
          "height": 15
        }
      },
      "ERMS": {
        "ERMS": {
          "pcolor": "rgb(255,0,255)",
          "pcolor2": "rgb(255,0,255)",
          "scale": {
            "max": 200,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast39-H3K4me3.bw",
          "height": 15
        }
      },
      "NB": {
        "NB": {
          "pcolor": "rgb(255,0,255)",
          "pcolor2": "rgb(255,0,255)",
          "scale": {
            "max": 200,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast3-H3K4me3.bw",
          "height": 15
        }
      },
      "ARMS": {
        "ARMS": {
          "pcolor": "rgb(255,0,255)",
          "pcolor2": "rgb(255,0,255)",
          "scale": {
            "max": 200,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast60-H3K4me3.bw",
          "height": 15
        }
      }
    },
    "H3K9-14Ac": {
      "config": {
        "pcolor": "255,0,51",
        "type": "bigwig",
        "height": "10"
      },
      "OS": {
        "OS": {
          "pcolor": "rgb(255,0,51)",
          "pcolor2": "rgb(255,0,51)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast22-H3K9-14Ac.bw",
          "height": 15
        }
      },
      "ERMS": {
        "ERMS": {
          "pcolor": "rgb(255,0,51)",
          "pcolor2": "rgb(255,0,51)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast39-H3K9-14Ac.bw",
          "height": 15
        }
      },
      "NB": {
        "NB": {
          "pcolor": "rgb(255,0,51)",
          "pcolor2": "rgb(255,0,51)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast3-H3K9-14Ac.bw",
          "height": 15
        }
      },
      "ARMS": {
        "ARMS": {
          "pcolor": "rgb(255,0,51)",
          "pcolor2": "rgb(255,0,51)",
          "scale": {
            "max": 50,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast60-H3K9-14Ac.bw",
          "height": 15
        }
      }
    },
    "H3K9me2": {
      "config": {
        "pcolor": "255,153,51",
        "type": "bigwig",
        "height": "10"
      },
      "OS": {
        "OS": {
          "pcolor": "rgb(255,153,51)",
          "pcolor2": "rgb(255,153,51)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast22-H3K9me2.bw",
          "height": 15
        }
      },
      "ERMS": {
        "ERMS": {
          "pcolor": "rgb(255,153,51)",
          "pcolor2": "rgb(255,153,51)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast39-H3K9me2.bw",
          "height": 15
        }
      },
      "NB": {
        "NB": {
          "pcolor": "rgb(255,153,51)",
          "pcolor2": "rgb(255,153,51)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast3-H3K9me2.bw",
          "height": 15
        }
      },
      "ARMS": {
        "ARMS": {
          "pcolor": "rgb(255,153,51)",
          "pcolor2": "rgb(255,153,51)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast60-H3K9me2.bw",
          "height": 15
        }
      }
    },
    "H3K9me3": {
      "config": {
        "pcolor": "102,102,255",
        "type": "bigwig",
        "height": "10"
      },
      "OS": {
        "OS": {
          "pcolor": "rgb(102,102,255)",
          "pcolor2": "rgb(102,102,255)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast22-H3K9me3.bw",
          "height": 15
        }
      },
      "ERMS": {
        "ERMS": {
          "pcolor": "rgb(102,102,255)",
          "pcolor2": "rgb(102,102,255)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast39-H3K9me3.bw",
          "height": 15
        }
      },
      "NB": {
        "NB": {
          "pcolor": "rgb(102,102,255)",
          "pcolor2": "rgb(102,102,255)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast3-H3K9me3.bw",
          "height": 15
        }
      },
      "ARMS": {
        "ARMS": {
          "pcolor": "rgb(102,102,255)",
          "pcolor2": "rgb(102,102,255)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast60-H3K9me3.bw",
          "height": 15
        }
      }
    },
    "INPUT": {
      "config": {
        "pcolor": "0,0,0",
        "type": "bigwig",
        "height": "10"
      },
      "OS": {
        "OS": {
          "pcolor": "rgb(0,0,0)",
          "pcolor2": "rgb(0,0,0)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast22-INPUT.bw",
          "height": 15
        }
      },
      "ERMS": {
        "ERMS": {
          "pcolor": "rgb(0,0,0)",
          "pcolor2": "rgb(0,0,0)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast39-INPUT.bw",
          "height": 15
        }
      },
      "NB": {
        "NB": {
          "pcolor": "rgb(0,0,0)",
          "pcolor2": "rgb(0,0,0)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast3-INPUT.bw",
          "height": 15
        }
      },
      "ARMS": {
        "ARMS": {
          "pcolor": "rgb(0,0,0)",
          "pcolor2": "rgb(0,0,0)",
          "scale": {
            "max": 20,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast60-INPUT.bw",
          "height": 15
        }
      }
    },
    "RNAPolII": {
      "config": {
        "pcolor": "0,0,255",
        "type": "bigwig",
        "height": "10"
      },
      "OS": {
        "OS": {
          "pcolor": "rgb(0,0,255)",
          "pcolor2": "rgb(0,0,255)",
          "scale": {
            "max": 100,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast22-RNAPolII.bw",
          "height": 15
        }
      },
      "ERMS": {
        "ERMS": {
          "pcolor": "rgb(0,0,255)",
          "pcolor2": "rgb(0,0,255)",
          "scale": {
            "max": 100,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast39-RNAPolII.bw",
          "height": 15
        }
      },
      "NB": {
        "NB": {
          "pcolor": "rgb(0,0,255)",
          "pcolor2": "rgb(0,0,255)",
          "scale": {
            "max": 100,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast3-RNAPolII.bw",
          "height": 15
        }
      },
      "ARMS": {
        "ARMS": {
          "pcolor": "rgb(0,0,255)",
          "pcolor2": "rgb(0,0,255)",
          "scale": {
            "max": 100,
            "min": 1
          },
          "file": "files/hg19/rhb-mast-nature2017/CHIPSEQ/Mast60-RNAPolII.bw",
          "height": 15
        }
      }
    },
    "browserview": {
      "nativetracks": [
        "RefGene"
      ],
      "nobox": 1,
      "position": {
        "chr": "chr11",
        "start": 17729012,
        "stop": 17752317,
        "gene": "MYOD1"
      },
      "tracks": [
        {
          "type": "profilegenevalue",
          "genevaluetklst": [
            {
              "name": "FPKM",
              "file": "files/hg19/rhb-mast-nature2017/fpkm.gz",
              "matchname": "sampleID"
            }
          ],
          "legendimg": {
            "file": "files/hg19/rhb-mast-nature2017/chromhmm.png",
            "width": 610,
            "height": 492
          },
          "name": "MAST chromHMM",
          "tracks": [
            {
              "type": "bedj",
              "file": "files/hg19/rhb-mast-nature2017/mast39.gz",
              "stackheight": 20,
              "stackspace": 1,
              "onerow": 1,
              "sampleID": "MAST 39",
              "name": "ERMS"
            },
            {
              "type": "bedj",
              "file": "files/hg19/rhb-mast-nature2017/mast60.gz",
              "stackheight": 20,
              "stackspace": 1,
              "onerow": 1,
              "sampleID": "MAST 60",
              "name": "ARMS"
            },
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Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors

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