Introduction To MetastaticCancer B37
From Array Suite Wiki
A metastatic cancer, is one which has spread from the primary site of origin (where it started) into different area(s) of the body (often by way of the lymph system or bloodstream). The liver, lungs, lymph nodes, and bones are common areas of spread or metastasis. Treatment of metastatic cancer depends on the type of cancer, where it started, the size and location of the metastasis, and other factors. MetastaticCancer_B37 Land contains the most common metastatic cancers, including bladder cancer, breast cancer, colon cancer, kidney cancer, lung cancer, melanoma, ovarian cancer, pancreas cancer, colorectal cancer, prostate cancer, stomach cancer, thyroid cancer, etc. The data types including array expression data, corresponding SNP6.0, and human Methylation 450 data. Data has been processed using the same genome build: Human.B37.3 and gene model: OmicsoftGene20130723
Raw Data are downloaded from GEO
- microarray platforms (including Affymetrix and Illumina)
- Copy number variation
- Methylation450 BeadChip
Expression Data: Omicsoft Affymetrix Microarray Preprocessing
Key Meta Data Columns
MetastaticCancer is curated at the comparison, sample and project level, using a controlled vocabulary for meta data to easily find and group data at all three levels.
- Comparison Cutoffs: Sample size, fold change, p value and expression cutoffs for each comparison.
- Comparison details: Comparison Category, Contrast, case and control sample IDs.
- DiseaseCategory (controlled vocabulary) : Disease category of the sample based on the details disease state.
- Land Sample Type: A detailed description of the cell type from which the cell line was derived, using OmicSoft's curation Controlled Vocabulary
- 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.
The most common way to research the data is to examine gene expression levels across sample meta data or other genomic features.
MetastaticCancer 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.
CD274 (PD-1L) gene expression grouped by treatment (Sampling time) in project GSE54323.
OncoGEO 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
CD274 (PD-1L) comparison view for Disease vs Normal comparisons in MetastaticCancer Land