CellLine NCI B37

From Array Suite Wiki

Jump to: navigation, search


CellLine NCI B37

The NCI-60 is a panel of 60 diverse human cancer cell lines used by the Developmental Therapeutics Program of the U.S. National Cancer Institute to screen over 100,000 chemical compounds and natural products (since 1990).

Land Version Genome Build Gene Model
CellLine_NCI_B37 Human.B37.3 OmicsoftGene20130723

Data Source

Data source: http://discover.nci.nih.gov/cellminer/home.do

Data Types

  • CNV, based on Affymetrix CEL files (downloaded)
  • DNASeq_Mutation (VCF files)
  • Expression Intensity Probes (Affymetrix)

Laboratory Methods

  • Affymetrix Expression Array

Processing Methods

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
[back to top]

Primary Grouping

Primary Site

Sample Distribution by Primary Site

Primary site NCI.png

[back to top]

Key Views

Gene Expression

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 EGFR.

[back to top]

DNA Mutation

Multiple visualizations display frequency and locations of gene mutations in CCLE samples, including the Mutation Landscape View.

Mutation landscape.png

DNA Mutation Landscape of Gene EGFR

[back to top]

Copy Number Variation

Copy number data can be visualized for a gene of interest, grouped by any metadata column, such as Histology.

Copy number NCI.png

Copy Number Log2 Ratio For EGFR, grouped by histology type

[back to top]

Related Articles