Consensus normalized expression (NX) levels were created for the 10 brain regions by combining the data from two transcriptomics datasets (GTEx and FANTOM5). Color coding is based on brain region and the bar shows the highest expression among the subregions included. To access sample data, click on region name or bar.

Read more about how the datasets were combined into consensus normalized expression levels in Assays & Annotation.

GTEx dataset
RNA-seq tissue data generated by the Genotype-Tissue Expression (GTEx) project is reported as mean pTPM (protein-coding transcripts per million), corresponding to mean values of the different individual samples for respective subregion. Highest expression among the subregions represents the brain region. To access sample data, click on region name or bar.

The GTEx RNA-seq assay is described in detail in Assays & Annotation.

FANTOM5 dataset
Tissue data for RNA expression obtained through Cap Analysis of Gene Expression (CAGE) generated by the FANTOM5 project are reported as Scaled Tags Per Million. To access sample data, click on region name or bar.

The CAGE method is described in detail in Assays & Annotation.

HPA Prefrontal cortex dataset
This dataset is a stand-alone dataset not integrated with other human transcriptomics data presented in the brain atlas. Brain expression data obtained through RNA-seq generated by the HPA, reported as normalized expression (NX) for human prefrontal cortex samples. Color coding of the bars separates prefrontal cortex and the three reference cortex regions (frontal, parietal and temporal). Trimmed mean values are calculated for the different subregions, to access individual sample data, click on subregion name or bar.

Read more about data normalization strategy and the prefrontal cortex sampling in Assays & Annotation.

HPA Pig dataset
HPA RNA-seq tissue data is reported as mean NX (normalized expression) for the 10 brain regions. The NX calculation is based on pTPM (protein-coding transcripts per million) of the individual samples, avaliable at the detaile pages (reached when clicking a bar or regional name).
To access sample data, click on region name or bar.

The HPA RNA-seq assay is described in detail in Assays & Annotation.

The pig brain transcriptomics project is a collaborative project between human protein atlas and the Lars Bolund institute of regenerative Medicine (Dr. Yonglun Luo), BGI-Qingdao, China.

HPA Mouse dataset
HPA RNA-seq tissue data is reported as mean NX (normalized expression) for the 10 brain regions. The NX calculation is based on pTPM (protein-coding transcripts per million) of the individual samples, avaliable at the detaile pages (reached when clicking a bar or regional name).
To access sample data, click on region name or bar.

The HPA RNA-seq assay is described in detail in Assays & Annotation.

The Allen Mouse Brain ISH
The expression values based on in situ hybridization (ISH) available through the ABA API (© 2004 Allen Institute for Brain Science, Allen Mouse Brain Atlas) is imported and show regional expression grouped in the same manner as the other datasets.
To access sample data and links to the ABA, click on region name or bar.

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