Pediatrics

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Pediatrics_B37

PediatricCancer_B37 Land includes a collection of the most common cancers in children including Childhood leukemia/lymphomas, Brain tumors, Neuroblastoma, Wilms tumor, Rhabdomyosarcoma, Retinoblastoma, Osteosarcoma, Ewing sarcoma, Germ cell tumors, etc.


Data Source

Treehouse Childhood Cancer Initiative

GEO

Land Version Genome Build Gene Model
B37 Human.B37.3 OmicsoftGene20130723

Data Types

  • Microarray platforms (including Affymetrix and Illumina)
  • Copy number variation

Processing Methods

Expression Data

Omicsoft Affymetrix Microarray Preprocessing

DNA-seq data

Omicsoft does not reprocess other genomic data, but extracts data directly from original datasets.

Key Meta Data Columns

Sample level:

  • DiseaseCategory (controlled vocabulary) : Disease category of the sample based on the details disease state. (primary grouping)
  • Land Sample Type: A detailed description of the cell type from which the cell line was derived, using OmicSoft's curation Controlled Vocabulary (secondary grouping)
  • TissueCategory (controlled vocabulary) : Tissue category such as skin, muscle, heart, kidney etc.
  • DiseaseState (controlled vocabulary) : Curated at sample level from each project.
  • SampleSource (controlled vocabulary) : Either cell type or tissue information. When a sample has cell type information, cell type is used. Otherwise, tissue category is used.
  • Land Tissue: The tissue from which the cell line was derived, using OmicSoft's curation Controlled Vocabulary
  • Tumor or Normal: Indicates whether a sample is from a tumor or normal sample.

Project level:

  • ProjectName: The name of individual projects where the data is from.
  • TherapeuticArea: Specific clinical focus of individual project (can be multiple areas depending on project)


Comparison level:

  • Comparison Cutoffs: Sample size, fold change, p value and expression cutoffs for each comparison.
  • Comparison details: Comparison Category, Contrast, case and control sample IDs.


Key Views

Gene Expression

The most common way to research the data is to examine gene expression levels across sample meta data or other genomic features.

Fgfr1 pediatricCancer.png

Project View

OncoGEO Land is a collection of individual GEO projects. Experimental designs in projects can be different, and batch effects in microarray projects, for example, are difficult to remove. OmicSoft created project-specific views to display expression values based on experiment design in each project.

Fgfr1 pediatricCancer project.png

fgfr1 gene expression grouped by DiseaseState in project GSE11024.

Comparison View

Pediatrics Land provides comparison views for projects with gene expression comparison results. By searching a gene, user can "visualize" the association (fold change by p-value) with the comparisons across projects, and narrow down to find interesting projects interactively. Comparison view is Omicsoft's highlight view, especially for Omicsoft DiseaseLand. For more details, please refer to: ComparisonLand

Fgfr1 pediatricCancer comparison.png

FGFR1 Treatment vs Control Comparison View.

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