The human protein atlas blog


Transcriptomics data from FANTOM program

2017-02-13
RNA RNA-seq Transcriptome Transcriptomics


Overview of the tissues and organs analysed by HPA, FANTOM and GTEx

In the latest version of the Human Protein Atlas, released in December 2016, the tissue atlas data is complemented with RNA-data from The Functional Annotation of Mammalian Genomes 5 (FANTOM5) project in RIKEN, Japan. The FANTOM data greatly overlaps with the Human Protein Atlas data, strengthening the results from both the projects.

The human genome consists of DNA which is transcribed into functional protein-coding transcripts (mRNA) and in turn is translated into proteins, the functional building-blocks of the cell. The entirety of mRNA molecules in a cell or tissue is called the "transcriptome". Knowing the transcriptome profiles of all the major tissues and organs in the human body can greatly increase our understanding of human biology, aid with disease state diagnosis, and help identify potential drug target candidates.

Many genome-wide transcriptome profiling technologies have been developed for identification and quantification of global gene expression, each emphasizing specific aspects of the mRNA transcripts. The RIKEN-based FANTOM5-consortium uses Cap Analysis of Gene Expression (CAGE), a Next Generation Sequencing based technique different from the RNA-Seq technique used within the Human Protein Atlas project. The expression profiles and functional annotations of mammalian cell-type specific transcriptomes prepared within FANTOM5 are based on a series of full-length cDNA technologies that have been developed by RIKEN.

In the new version of the Human Protein Atlas, CAGE data for 35 tissues was obtained from the FANTOM5 repository and compared to the data in the Human Protein Atlas. As expected, both data sets show considerable similarity but also allow novel insights due to their complementary nature.

"The data from FANTOM5 overlaps with our datasets on the RNA-level, but there is also a good correlation on the protein-level. This is very positive and strengthens the results from both the projects," says Mathias Uhlen, professor at KTH and director of the Human Protein Atlas. "The integration of large data sets from different international consortia allows researchers around the world to explore what proteins are present in different human cells, tissues and organs and these repositories can also be used to increase our molecular understanding of disease and other biological processes such as aging."

"One of the goals of FANTOM5 is to comprehensively map transcriptional regulatory networks of protein coding genes and regulatory non-coding RNA. We are totally pleased that our genomic datasets were instrumental to complement expression analysis for the Human Protein Atlas," says Piero Carninci from RIKEN Center for Life Science Technologies, one of the leaders of FANTOM5.


Frida Henningson Johnson