The cell line section - Explore the expression profiles in human cell lines

The Cell Line section contains information on genome-wide RNA expression profiles of human protein-coding genes in 1055 human cell lines, including 985 cancer cell lines. The transcriptomics analysis includes classification based on specificity analysis across 27 cancer types, distribution and expression cluster analysis across all cell lines and for selected cancer types also analysis of similarity of the cell lines to their corresponding cancer type. More information about the specific content and the generation and analysis of the data in the section can be found in the Methods summary.

Learn about:

  • if a gene is enriched in cellines from a particular cancer type (specificity)
  • which genes have a similar expression profile across the cell lines (expression cluster)
  • the catalogue of genes elevated in each of the cell lines
  • which cell line has the most consistent expression profile to its corresponding TCGA disease cohort (i.e., the best cell lines for cancer study)
  • cancer-related pathway and cytokine activity of each cell line


CELL LINE TYPES

The 1055 different cell lines used in the Cell Line section have been selected to represent various cell populations in different tissue types and organs of the human body. Most of the cell lines used are human cancer cell lines (n = 985). In addition to the cancer-derived cell lines, there is a number of cell lines that have been generated through in vitro protocols for immortalization of normal cells, some primary cell lines and one type of induced pluripotent stem cells.

Click on the different cancer types to find the data for and more details regarding the features and origin of the related cell lines, or find the cell line of interest in the complete list of cell lines. For cell lines associated with cancer types also analysed in the Pathology section, the similarity of the cell lines to their corresponding TCGA cancer type is provided to help researchers select the best cell lines for in vitro cancer study. The related cancer types are found in the left part of the cell line box below.


CELL LINE EXPRESSIONi

The RNA data was used to cluster genes according to their expression across cell lines. The clustering of 19466 genes expressed in cell lines resulted in 69 expression clusters, which have been manually annotated to describe common features in terms of function and specificity. The result of the cluster analysis is presented as a UMAP based on gene expression, where each cluster has been summarized as colored areas containing most of the cluster genes.

Go to interactive expression cluster page

CELL LINE SPECIFICITYi

Classification of all protein-coding genes based on RNA expression in cell lines, determining the number of genes enriched, group enriched or elevated in a particular cancer types compared to all other cancer types. Click in the piechart or on the bars to generate lists of corresponding genes.

CELL LINE ENRICHMENTi

In the figure all genes enriched in cell lines corresponding to a maximum of two cancer types are displayed. Click on the numbers to obtain the corresponding list of genes.

Contact

The Project

The Human Protein Atlas

The Human Protein Atlas project is funded
by the Knut & Alice Wallenberg Foundation.