The 12th release of the Human Protein Atlas (HPA) covers 16,621 genes (approximately 83% of the human protein-coding genes) and includes protein expression profiles based on 21,984 antibodies. A major restructuring of the knowledge portal has been done with the release of four separate sub-atlases; Normal tissue atlas, Subcellular atlas, Cell line atlas and Cancer atlas, and RNA transcript data has been added for a majority of the tissues in the normal tissue atlas and the cells in the cell line atlas.
The normal tissue atlas is the largest of the four sub-atlases and contains more than 13 million images of protein profiling in 46 human tissues of different origin. The atlas now also includes RNA transcript data for 27 of these organ-specific tissues using next generation sequencing, providing a tissue distribution map of both protein and gene expression.
“We are truly excited about the RNA transcript data and the map of gene expression that we now have for 27 different organ-specific tissues”, says Professor Mathias Uhlén, Program Director of the Human Protein Atlas. “This data allows classification of all human protein-coding genes into those coding for house-hold functions (present in all cells) and those that are tissue-specific genes with highly specialized expression in particular organs and tissues, such as kidney, liver, brain, heart, pancreas. This is interesting starting points for all researchers interested in human biology and disease”.
The work is carried out at the Science for Life Laboratory (SciLifeLab) in Stockholm and Uppsala. Access to advanced high-throughput instruments for next generation sequencing at SciLifeLab has enabled the very fast process of adding transcript data to the protein atlas.
“The RNA transcript data has been really helpful in regards to proteins that are completely unknown”, says Caroline Kampf, Associate professor and site director HPA Uppsala. The main focus for the Uppsala group is to validate protein expression in human tissues and cells.
The project behind the Human Protein Atlas started as a small research project at KTH Royal Institute of Technology in the research group of Professor Mathias Uhlén in 2000. Since 2003, the non-profit Knut and Alice Wallenberg Foundation has been the major funding agency for this project involving more than 150 scientists in 17 countries. The protein atlas is (www.proteinatlas.org)
a publically available portal for researchers in life sciences and provides access to protein profiling data in 46 normal tissues, 20 cancer tissues, 46 cell lines and on a subcellular level. The gene-centric visualization with data covering a majority of the human protein-coding genes is now complemented with RNA transcript data.
The release of the protein atlas is accompanied with a publication in Mol. Cell. Proteomics (Fagerberg et al, “Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics”) with a focus in the article on the tissue-specific pattern in the human body.
Mathias Uhlén, Professor, KTH Royal Institute of Technology, Science for Life Laboratory
Phone: +46-8-5537 8403 (secr)
Caroline Kampf, Associated Professor, Uppsala University, Science for Life Laboratory
Phone: +46 18 471 50 32
Science for Life Laboratory
Tel: +46 8 524 81510
Science for Life Laboratory (SciLifeLab) is a national center for molecular biosciences with focus on health and environmental research. The center combines frontline technical expertise with advanced knowledge of translational medicine and molecular bioscience. SciLifeLab is a national resource and a collaboration between four universities: Karolinska Institutet, KTH Royal Institute of Technology, Stockholm University and Uppsala University.