QSP modeling tool - how can we download data from CYTOCON DB to obtain averaged cytokines and neutrophils concentrations for healthy subjects tissues

Ekaterina Mogilevskaya
March 1, 2023


CYTOCON DB is a manually curated online database of human baseline concentrations of cytokines and cells measured in different tissues of healthy subjects and patients suffering from various pathologies. The Query page allows a user to download the data on one or more molecules/cells choosing tissues and diseases. Most baseline values found in papers were converted from original units (i.e., mg/ml, number of cells per mm2 of biopsy surface section) to unified units: “pM” for cytokine and “kcell/L” for cell concentration. Formulas for the conversion were implemented in the database. More info about CYTOCON DB and examples of its application in data analysis and QSP projects can be found in our paper: CYTOCON: The manually curated database of human in vivo cell and molecule concentrations CPT Pharmacometrics Syst Pharmacol. 2022 Sep 21. doi: 10.1002/psp4.12867

Objective: to download data on healthy subjects neutrophils and molecules concentrations from CYTOCON DB.

Let’s download neutrophils concentrations in healthy subjects blood from the DB. We should open the Query page and choose Cell, Neutrophils, Blood, Healthy control:

And press the Query button. So we get the table with the results:

The data are presented in the table in both original and unified units, so they can be easily compared and further analyzed.

Pressing “Export to CSV” button we obtain Excel-file with all the information on each concentration from an article – average, dispersion, min, max values in original and unified units; experimental methods, article links, patient groups attributes (patient, male, female number, average age, BMI, ESR, inclusion-exclusion criteria etc.); disease attributes (FEV1,HCV,HPV-seropositivity, etc.)

Moreover, we can press “Graph result” button and obtain graphical representation of the results in unified units:

On this graph averages and dispersions are presented for each patient group from a number of articles.

In the same way we downloaded data tables for neutrophils in bone marrow and tissues (bronchial submucosa, airway smooth muscle, bronchial glands, lung tissue, epidermis, dermis).

Also we downloaded molecule concentrations in serum. For example, here is the query for IL6:

The table results for IL6 looks in a following way:

Similarly, we downloaded the concentrations for other molecules in serum, tissues, bone marrow and lymph node.

Further we averaged the values in unified units for each cell/molecule in each tissue and find min and max values. And presented this information as hystograms for cells:

And for molecules:


The presented example illustrates that CYTOCON DB allows to download the data on separate cells/molecules in chosen tissues/diseases. The process is fast and convenient, and the information collected in the database enables users to save time in QSP modeling typically spent on gathering and processing of literature and available data.

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