From Array Suite Wiki
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.
|Land Version||Genome Build||Gene Model|
- Microarray platforms (including Affymetrix and Illumina)
- Copy number variation
Omicsoft does not reprocess other genomic data, but extracts data directly from original datasets.
Key Meta Data Columns
- 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.
- 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 Cutoffs: Sample size, fold change, p value and expression cutoffs for each comparison.
- Comparison details: Comparison Category, Contrast, case and control sample IDs.
The most common way to research the data is to examine gene expression levels across sample meta data or other genomic features.
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 gene expression grouped by DiseaseState in project GSE11024.
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 Treatment vs Control Comparison View.