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 69 human cell lines. The transcriptomics analysis includes classification based on specificity, distribution and expression cluster analysis across all cell lines. 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 a particular human cell line (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


The 69 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. Many of the cell lines used are human cancer cell lines, which in some aspects may limit their resemblance to normal human cells in the context of tissues and organs, but as seen in the UMAP plot based on RNA expression data below most cluster rather well according to origin and phenotype. 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. The highest level of separation is seen between cell lines growing adherent and in cell suspension, with the latter representing hematopoietic and lymphoid cell systems. The suspension cluster is further separated into two major clusters depending on myeloid or lymphoid origin/phenotype, and a schematic description of hematopoietic differentiation lineages including the cellular origin for related cell lines is shown here. Click on the different tissues below the plot to find more details regarding the features and origin of the related cellines or go to the complete list of cell lines.

BrainEndothelialEyeFemale reproductive systemGastrointestinal tractKidney & urinary bladderLiver & gallbladderLungLymphoidMale reproductive systemMesenchymalMuscleMyeloidPancreasProximal digestive tractSkin


The RNA data was used to cluster genes according to their expression across cell lines. The clustering of 18024 genes expressed in cell lines resulted in 44 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


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 cell line compared to all other cell lines. Click in the piechart or on the bars to generate lists of corresponding genes.


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