Visualization Community | St. Jude Cloud

PAX5-driven subtypes of B-progenitor acute lymphoblastic leukemia (GenomePaint)

St. Jude Children's Research Hospital

50 4

Jan 28, 2019

PMID 30643249

16.6K

Whole Genome Sequencing

Whole Exome Sequencing

RNA Sequencing

SNP Array

CNV log ratio is displayed for B-ALL subtypes (total number samples = 1988). Mousing over colored bars displays metadata for each sample. Additionally, you can download the gene expression values for all 1988 samples as log2(FPKM) (https://proteinpaint.stjude.org/ppSupport/static/hg19/pan-all/B-ALL-subtyping.FPKM-UQ10-log2.txt.zip), rlog values ( https://proteinpaint.stjude.org/ppSupport/static/hg19/pan-all/panALL-1988S-rlog.subtype.txt.gz), HTSeq raw read counts (https://proteinpaint.stjude.org/ppSupport/static/hg19/pan-all/BALL-1988S-HTSeq.zip) or HTSeq files for normal samples ( https://proteinpaint.stjude.org/ppSupport/static/hg19/pan-all/Normal.HTSeq.zip). Finally, you can download the gene expression signatures for each subtype here (https://proteinpaint.stjude.org/ppSupport/static/hg19/pan-all/B-ALL-subtype-signature.xlsx).

Loading Visualization

runproteinpaint({
  "host": "https://proteinpaint.stjude.org",
  "holder": visualizationContainer[0],
  "noheader": true,
  "parseurl": true,
  "genome": "hg19",
  "block": 1,
  "nativetracks": "RefGene",
  "nobox": 1,
  "position": "chr9:36698305-37354131",
  "datasetqueries": [
    {
      "dataset": "Pan-ALL",
      "querykey": "svcnv"
    }
  ]
});

Visualization Code

runproteinpaint({
  "host": "https://proteinpaint.stjude.org",
  "holder": visualizationContainer[0],
  "noheader": true,
  "parseurl": true,
  "genome": "hg19",
  "block": 1,
  "nativetracks": "RefGene",
  "nobox": 1,
  "position": "chr9:36698305-37354131",
  "datasetqueries": [
    {
      "dataset": "Pan-ALL",
      "querykey": "svcnv"
    }
  ]
});

PAX5-driven subtypes of B-progenitor acute lymphoblastic leukemia (GenomePaint)

Read more

Loading Visualization

Visualization Code