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General description of the gene and encoded protein(s) using information from HGNC and Ensembl, as well as predictions made as well as predictions made by the Human Protein Atlas project.
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 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
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.
Group enriched (hippocampal formation, midbrain, pons and medulla)
Region enriched (midbrain)
Regional distributioni
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.
Nucleus in neurons. Choroid plexus of ependymal cells.
Protein profilei
A summary of the overall protein localization across the analyzed brain tissue. The summary is based on manual annotation.
Mouse brain profiles includes a more extensive summary of the protein location while summaries with only human protein profile are more limited and are based on imported data/images from the Tissue Atlas stainings that has undergone an additional brain-centric curation step.
Pax5 is a transcription factor mainly expressed in the human spleen, appendix, lymph node and tonsil tissue, with extremely low levels in the CNS, according to available transcriptomic data. However, in the mouse, both RNA and protein data agree on an enrichment in parts of the midbrain, where a strong and dense neuronal nuclear staining is restricted to some distinct brain regions, like the parabrachial region, periaqueductal gray matter, mesenchephalic reticular formation and the substantia nigra. In the forebrain, sparse low or moderate-intensity neuronal nuclear immunostaining is noticed in the hippocampus while neuronal cell body staining is noticed in the dorsal taenia tecta.
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 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 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 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.
Non curated brain data available in the Tissue Atlas.
MOUSE BRAIN PROTEIN LOCATIONi
Mouse brain protein profiles are based in serial sections of the adult mouse brain analyzed by immunofuorescence. The staining intensity and regional distribution is manually summarized.
Pax5 is a transcription factor mainly expressed in the human spleen, appendix, lymph node and tonsil tissue, with extremely low levels in the CNS, according to available transcriptomic data. However, in the mouse, both RNA and protein data agree on an enrichment in parts of the midbrain, where a strong and dense neuronal nuclear staining is restricted to some distinct brain regions, like the parabrachial region, periaqueductal gray matter, mesenchephalic reticular formation and the substantia nigra. In the forebrain, sparse low or moderate-intensity neuronal nuclear immunostaining is noticed in the hippocampus while neuronal cell body staining is noticed in the dorsal taenia tecta.
Cellular location
Nucleus in neurons. Choroid plexus of ependymal cells.
Protein profile reliability
Supported based on HPA056394
HPA Mouse staining intesityi
The score is based on the relative fluorescence, defined as intensity of the annotated region relative to the intensity of the region with highest intensity. The digitalized images are processed (axel-adjusted and tissue edges defined) and regions of interest (ROIs) are then marked. These ROIs are then used for image analysis and the relative fluorescence intensity is listed for each region. For more data and regional information click on the bar or the regional name.
The Human Protein Atlas project is funded
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