The inclusion of transcriptome anaylsis dataset to the Human Protein Atlas database makes it even more comprehensive

from Health Canal –

Today, the 15th version of the Human Protein Atlas is launched. The new version includes data from different sources, which makes comparisons between tissue profiles on both the RNA and protein level possible.

Looking closely at healthy and sick conditions in the human tissues or cells makes it possible to learn more and thereby improve healthcare. To do this comparisons the researchers first need to know how the human body is built. One way is to analyze the transcriptome. This means looking into which genes are activated to create a protein in the tissue or cell sample.

The human biology is constructed in three steps; from DNA to RNA and then to protein. The DNA code needs to be copied to the RNA, and then read to make a protein. To detect and count protein molecules is very complicated and the scientists need different methods to make sure the data is valid. One way is to analyze the transcriptome to count the amount of RNA molecules being copied from the DNA of a certain gene, creating a picture of what proteins to expect from the sample. Counting RNA molecules is easier than counting protein molecules.

The Human Protein Atlas includes proteome analysis based on more than 25 000 antibodies targeting more than 17 000 unique proteins, combined with transcriptome analysis covering all 20 000 human protein coding genes. The new atlas launched on April 11 also includes primary data from several sources, which allows for comparisons.

The new version of the Human Protein Atlas is significantly advancing in terms of mapping the transcriptome in different human tissues. These data have been the basis for much of the metabolic modelling we are doing here at Chalmers. I am therefore very excited about the progress, and the Human Protein Atlas will certainly be an important resources in our aims to advance towards better diagnostics and precision medicine, says Professor Jens Nielsen at the Department of Biology and Biological Engineering.

Global transcriptomics analysis of human tissues and organs


Overview of the tissues and organs analyzed using RNA-seq by the Human Protein Atlas consortium (HPA, green), tissues studied with cap analysis gene expression (CAGE) within the FANTOM consortium (purple), and tissues analyzed using RNA-seq by the genome-based tissue expression consortium (GTEx, orange). Altogether, 22 tissues and organs were studied with both the HPA and FANTOM datasets, while 21 tissues overlapped between the HPA and GTEx datasets.

The launch is accompanied by an article in Molecular Systems Biology describing transcriptome resources with a focus on the comparison between the datasets generated from the Broad Institute, Boston, US (GTEx) and the Human Protein Atlas. The GTEx dataset includes more than 1600 samples from mostly overlapping, but in some cases unique, tissues compared to the Human Protein Atlas. RNA-seq data from 28 of the GTEx tissues with a corresponding tissue in Human Protein Atlas have been included to allow for direct comparisons between the Human Protein Atlas and GTEx data sets.

The inclusion of the GTEx dataset to the Human Protein Atlas database makes it even more comprehensive and it is reassuring that there is a significant overlap in the tissue classification of the genes based on the two independent datasets, says Professor Mathias Uhlén, program director for the Human Protein Atlas project.

The article published in Molecular Systems Biology discusses publicly available human transcriptome resources and the possible use of these databases for various applications, such as building genome-scale metabolic models used for analyzing cell and tissue functions both in health an disease contexts.

Visit your favorite gene to browse our new layout on the Tissue Atlas!

Here is one example: PRR4

About the Human Protein Atlas project
The Human Protein Atlas project is a major multinational project funded by the Knut and Alice Wallenberg Foundation. It has been set up to allow for a systematic exploration of the human proteome using antibody-based proteomics. This is accomplished by combining high-throughput generation of affinity-purified antibodies with protein profiling in a multitude of tissues and cells assembled in tissue microarrays. Confocal microscopy analysis using human cell lines is performed for more detailed protein localization. The program hosts the Human Protein Atlas portal with expression profiles of human genes and proteins in a multitude of tissues and cells. The project is a collaboration between AlbaNova and SciLifeLab, KTH – Royal Institute of Technology, Rudbeck Laboratory, Uppsala University and Chalmers.

Source – Health Canal

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