Introduction to Sanger Land Content
From Array Suite Wiki
Sanger_B37 and Sanger_B38
In order to improve their utility, the Sanger Cancer Genome Project has embarked on a systematic characterization of the genetics and genomics of large numbers of cancer cell lines.
Data source: Data source: COSMIC
|Land Version||Genome Build||Gene Model|
- DNA-Seq Mutation (Exome)
- Expression Intensity Probes (Affymetrix)
- Methylation450 Bead Chip
- Affymetrix Expression Array
Expression Data: Omicsoft Affymetrix Microarray Preprocessing
Key Meta Data Columns
- Primary Site: The body site where the cell line sample is derived from.
- Histology: Histological types of cancer, such as carcinoma, glioma and sarcoma.
- Land Tissue: The tissue from which the cell line was derived, using OmicSoft's curation Controlled Vocabulary
- Land Sample Type: A detailed description of the cell type from which the cell line was derived, using OmicSoft's curation Controlled Vocabulary
- TCGA Cancer Type: Descriptions of cancer types, matching "Disease" in TCGA
Sample Distribution by Primary Site
One of the most common ways to visualize gene expression data is a per-sample Scatter plot (Expression View), with each sample grouped by Primary Site on the Y-axis, and expression level plotted on the X-axis:
Expression profile of BRAF.
Mutation Site Distribution
Exome Sequencing mutation data can be queried and grouped by metadata columns. For example, it is clear from this graph that BRAF is highly mutated in skin cancers:
Note: in this view, all alleles will be plotted in separate charts (arrow indicates there are 62 alleles of BRAF found in this land). The mutation distribution view will show a summary of ALL mutations in the gene(s) queried.