All transcripts of all genes have been analyzed regarding the location(s) of corresponding protein based on prediction methods for signal peptides and transmembrane regions.
Genes with at least one transcript predicted to encode a secreted protein, according to prediction methods or to UniProt location data, have been further annotated and classified with the aim to determine if the corresponding protein(s) are secreted or actually retained in intracellular locations or membrane-attached.
Remaining genes, with no transcript predicted to encode a secreted protein, will be assigned the prediction-based location(s).
The annotated location overrules the predicted location, so that a gene encoding a predicted secreted protein that has been annotated as intracellular will have intracellular as the final location.
The internal antibody ID for the antibody/antibodies available for this specific target, click link for more antibody information.
No antibodies in assay
HUMAN PROTEIN ATLAS INFORMATION
The RNA specificity category is based on mRNA expression levels in the analyzed samples based on a combination of data from HPA, GTEX and FANTOM5. The categories include: tissue enriched, group enriched, tissue enhanced, low tissue specificity and not detected. The Tissue classification is based on 37 human tissue types, where brain is represented by the highest expression value among the human brain regions (including spinal cord and corpus callosum that is excluded from the regional classification based on 10 main brain regions). The combination of tissue and regional classification can be found here
Group enriched (esophagus, intestine, lymphoid tissue, tongue)
The regional specificity category is based on mRNA expression levels in the analyzed brain samples, grouped into 10 main brain regions and calculated for the three different species. The human brain expression profile is based on a combination of data from GTEX and FANTOM5. The specificity categories include: regionally enriched, group enriched, regionally enhanced, low regional specificity and not detected. The classification rules are the same used for the tissue specificity category.
The regional distribution category is based on mRNA expression detected above cut off or not in the analyzed brain samples, grouped into 10 main brain regions and calculated for the three different species. The human brain expression is based on a combination of data from GTEX and FANTOM5. The distribution categories include: detected in all, detected in many, detected in some, detected in single and not detected. The classification rules are the same used for the tissue distribution category.
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 Human brain RNA-Seq dataseti
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.
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.
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.
HUMAN BRAIN PROTEIN LOCATIONi
The Human brain protein data is based on curated and manually selected Tissue Atlas data. The standard brain regions used in the Tissue Atlas are cerebral cortex, caudate nucleus, hippocampus and cerebellum, only selected cases include information on hypothalamus or retina. The score is based on knowledge-based annotation of the protein location in the main cell types. For genes where more than one antibody has been used, a collective score is set displaying the estimated true protein expression.