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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.
Number of protein-coding transcribed from this gene as defined by Ensembl.
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HUMAN PROTEIN ATLAS INFORMATIONi
The Tissue Atlas contains information regarding the expression profiles of human genes both on the mRNA and protein level. The protein expression data from 44 normal human tissue types is derived from antibody-based protein profiling using immunohistochemistry.
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 RNA distribution 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: detected in all, detected in many, detected in some, detected in single and not detected.
Protein evidence scores are generated from several independent sources and are classified as evidence at i) protein level, ii) transcript level, iii) no evidence, or iv) not available.
Evidence at protein level
Protein expressioni
A summary of the overall protein expression pattern across the analyzed normal tissues. The summary is based on knowledge-based annotation.
"Estimation of protein expression could not be performed. View primary data." is shown for genes analyzed with a knowledge-based approach where available RNA-seq and gene/protein characterization data has been evaluated as not sufficient in combination with immunohistochemistry data to yield a reliable estimation of the protein expression profile.
Standardized explanatory sentences with additional information required for full understanding of the protein expression profile, based on knowledge-based and secretome-based annotation.
Antibody staining mainly not consistent with RNA expression data. Pending external verification.
Reliability scorei
A reliability score is manually set for all genes and indicates the level of reliability of the analyzed protein expression pattern based on available RNA-seq data, protein/gene characterization data and immunohistochemical data from one or several antibodies with non-overlapping epitopes. The reliability score is based on the 44 normal tissues analyzed, and if there is available data from more than one antibody, the staining patterns of all antibodies are taken into consideration during evaluation.
The reliability score is divided into Enhanced, Supported, Approved, or Uncertain, and is displayed on both Tissue Atlas and Pathology Atlas.
Below is an overview of RNA and protein expression data generated in the Human Protein Atlas project. Analyzed tissues are divided into color-coded groups according to which functional features they have in common. For each group, a list of included tissues is accessed by clicking on group name, group symbol, RNA bar, or protein bar. Subsequent selection of a particular tissue in this list links to the image data page.
Images of selected tissues give a visual summary of the protein expression profile furthest to the right.
The gray human body provides links to a histology dictionary when clicking on any part of the figure.
Expression
Detection
All organs
RNA expression (NX)i
RNA expression summary shows the consensus RNA-data based on normalized expression (NX) data from three different sources: internally generated Human Protein Atlas (HPA) RNA-seq data, RNA-seq data from the Genotype-Tissue Expression (GTEx) project and CAGE data from FANTOM5 project. Color-coding is based on tissue groups, each consisting of tissues with functional features in common. To access sample data, click on tissue name or bar.
Each bar represents the highest expression score found in a particular group of tissues. Protein expression scores are based on a best estimate of the "true" protein expression from a knowledge-based annotation, described more in detail under Assays & annotation. For genes where more than one antibody has been used, a collective score is set displaying the estimated true protein expression.
Protein expression data is shown for each of the 44 tissues. Color-coding is based on tissue groups, each consisting of tissues with functional features in common. Mouse-over function shows protein score for analyzed cell types in a selected tissue. To access image data click on tissue name or bar. Annotation of protein expression is described in detail in Assays & annotation.
For genes with available protein data for which a knowledge-based annotation gave inconclusive results, no protein expression data is displayed in the protein expression data overview. However, all immunohistochemical images are still available and the annotation data can be found under Primary data.
Organ
Expression
Alphabetical
RNA EXPRESSION OVERVIEWi
RNA expression overview shows RNA-data from three different sources, respectively: Internally generated Human Protein Atlas (HPA) RNA-seq data, RNA-seq data from the Genotype-Tissue Expression (GTEx) project and CAGE data from FANTOM5 project, as well as the consensus dataset which is based on a combination of all three sources. Color-coding is based on tissue groups, each consisting of tissues with functional features in common. To access sample data, click on tissue name or bar.
Consensus dataset Consensus Normalized eXpression (NX) levels for 55 tissue types and 6 blood cell types, created by combining the data from the three transcriptomics datasets (HPA, GTEx and FANTOM5) using the internal normalization pipeline. Color-coding is based on tissue groups, each consisting of tissues with functional features in common. To access sample data, click on tissue name or bar.
Read more about how the datasets were combined into consensus normalized expression levels in Assays & Annotation.
Organ
Expression
Alphabetical
RNA tissue specificity: Low tissue specificity
HPA dataseti
HPA dataset HPA RNA-seq tissue data is reported as mean pTPM (protein-coding transcripts per million), corresponding to mean values of the different individual samples from each tissue. Color-coding is based on tissue groups, each consisting of tissues with functional features in common. To access sample data, click on tissue name or bar.
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 from each tissue. Color-coding is based on tissue groups, each consisting of tissues with functional features in common. To access sample data, click on tissue 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. Color-coding is based on tissue groups, each consisting of tissues with functional features in common. To access sample data, click on tissue name or bar.
For selected proteins extended tissue profiling is performed in addition to standard tissue microarrays. The section below contains results from the extended profiling.
SPCS3 is associated with 2 reactions in 1 different subsystems: Cytosol, Endoplasmic reticulum, Mitochondria, Nucleus, Peroxisome.
Provided by metabolicatlas.org
The Human Protein Atlas project is funded
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