Cell type enriched genes

We developed a novel analysis method to identify endothelial enriched genes (genes that are most highly expressed in this cell type, compared to others) through the deconvolution of unfractionated RNAseq data from multiple different human organs. Using this method, we published the first description of core human endothelial specific genes, which are now often used as a reference set for other deconvolution studies. As endothelial cells are known to differ significantly between tissue beds, with specialised functions depending on location, we have now expanded the analysis to investigate expression profiles in different organs. Using the human brain as a ´test case´ we showed a high level of consistency between our results and those from single cell RNAseq analysis, and the applicability of using this method to compare endothelial profiles in healthy and diseased tissue.

More recently, using the same analysis method, we have profiled the major cell types from 15 different tissue types, data which features on the Human Protein Atlas web page in the ´Tissue Cell Type´ section

Associated publications and pre-prints:

Butler LM, Hallström BM, Fagerberg L, Pontén F, Uhlén M, Renné T, Odeberg J (2016). Analysis of body-wide unfractionated tissue data to identify a core human endothelial transcriptome. Cell Systems 3(3) 287-30

Dusart P, Hallström BM, Renné T, Odeberg J, Uhlén M, Butler LM (2019) A systems-based map of human brain cell-type enriched genes and malignancy-associated endothelial changes. Cell Reports 29(6) 1690-1706

Norreen-Thorsen M, Struck EC, Öling S, Zwahlen M, Von Feilitzen K, Odeberg J, Lindskog C, Pontén F, Uhlén M, Dusart PJ, Butler LM (2022) A human adipose transcriptome atlas. Cell Reports 40(2):111046

Öling S, Struck E, Norreen-Thorsen, M, Zwahlen M, von Feilitzen K, Odeberg J, Pontén F, Lindskog C, Uhlén M, Dusart P, Butler LM. A human stomach cell type transcriptome atlas. Pre-print on biorxiv.org

Dusart P, Öling S, Struck E, Norreen-Thorsen, M, Zwahlen M, von Feilitzen K, Oksvold P, Bosic M, MJ Iglesias MJ, Renne T, Odeberg J, Pontén F, Lindskog C, Uhlén M, Butler LM. A tissue centric atlas of cell type transcriptome enrichment signatures. Pre-print on biorxiv.org