The lung cancer cell line gene expression data was obtained from the Cancer Cell Line Encyclopedia (CCLE). Gene expression values were z-scored across all 1047 cancer cell lines in the CCLE. 37 of the 42 cell lines that were assayed by CST were also assayed by the CCLE.
We defined genes of interest based on two criteria
In order to capture genes with both of these properties we filtered for genes that: 1) were differentially expressed with a Z-score of absolute value at or above 3 in at least 4 cell lines, 2) we allowed users to filter for the top genes based on the sum of their gene expression across all cell lines (using filter sliders). This filtering leaves us with 215 genes of interest.
The interactive visualization can be seen here: CST_Lung_Cancer_Viz.
Several of the most-differentially expressed genes are known to be important in lung cancer and we will go over a few here.
NKX2-1 is the 4th most up-regulated gene from our filtered gene expression data (filtering described above). Below is a screenshot of the most up-regulated genes, where both the cell lines and genes have been ordered based on their sum. Red 'cells' in the clustergram indicate up-regulated expression of a gene in a cell line.
from IPython.display import Image
filename = 'img/NKX2-1_4th_most_up-regulated_gene_expression.png'
Image(filename=filename)
NKX2-1 is also thought to play a role in lung development Uniprot link.
The most up-regulated gene, SFTA3, is known to be highly expressed in the lung.
The presence of lung-associated genes in the list of most up-regulated genes indicates that the differential gene expression data from the CCLE is identifying functionally important genes.
SMARCA4 is the most down-regulated gene from our filtered gene expression data. Below is a screenshot of the most down-regulated genes, where both the cell lines and genes have been ordered based on their sum. Blue 'cells' in the clustergram indicate down-regulated epression of a gene in a cell line.
from IPython.display import Image
filename = 'img/SMARCA4_most_down-regulated_gene_expression.png'
Image(filename=filename)