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RNA category is based on mRNA expression levels in the analyzed samples (RNA assay description). The categories include: tissue/cell line enriched, group enriched, tissue/cell line enhanced, expressed in all, mixed and not detected. RNA category is calculated separately for The Cancer Genome Atlas (TCGA) data from cancer tissues and internally generated Human Protein Atlas (HPA) data from normal tissues and cell lines.
Group enriched (brain, caudate, cerebellum, esophagus, hippocampus, pituitary gland, tonsil)
Protein evidencei
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.
Nuclear expression in selected tissues, including CNS.
DATA RELIABILITY
Data reliability descriptioni
Standardized explanatory sentences with additional information required for full understanding of the knowledge-based expression profile.
Antibody staining mainly not consistent with RNA expression data. Cytoplasmic staining observed and disregarded.
Reliability scorei
Reliability score (score description), divided into Supported, Approved, or Uncertain, is evaluated in normal tissues and based on consistency between the staining pattern of one antibody or several antibodies with RNA-seq data and available gene/protein characterization data.
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.
RNA expression (TPM)i
RNA-seq results generated in HPA are reported as number of transcripts per million (TPM). Each bar represents the highest expression score found in a particular group of tissues. The assay is described more in detail in Assays & Annotation.
Protein expression (score)i
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. The color-coding is based on tissues with functional features in common. Mouse-over function shows protein score for analyzed cell types found 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: 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.
HPA dataseti
HPA dataset RNA-seq tissue data is reported as mean TPM (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. The RNA-seq assay is described in detail in Assays & Annotation.
RNA tissue category HPA HPA RNA tissue category (category description) is calculated based on mRNA expression levels across all tissues and include: tissue enriched, group enriched, tissue enhanced, expressed in all, mixed and not detected.
GTEx dataset RNA-seq data are reported as median RPKM (reads per kilobase per million mapped reads), generated by the Genotype-Tissue Expression (GTEx) project. More information can be found in Assays & Annotation.
RNA tissue category GTEx GTEx RNA tissue category (category description) is calculated based on mRNA expression levels across all tissues and include: tissue enriched, group enriched, tissue enhanced, expressed in all, mixed and not detected.
FANTOM5 dataset Tissue data obtained through Cap Analysis of Gene Expression (CAGE) are reported as Tags Per Million, generated by the FANTOM5 project. More information can be found in Assays & Annotation.
RNA tissue category FANTOM5 FANTOM5 RNA tissue category (category description) is calculated based on gene expression levels across all tissues and include: tissue enriched, group enriched, tissue enhanced, expressed in all, mixed and not detected.
Gene information from Ensembl and Entrez, as well as links to available gene identifiers are displayed here. Information was retrieved from Ensembl if not indicated otherwise.
Gene name
SOX2
Synonyms
Description
SRY (sex determining region Y)-box 2 (HGNC Symbol)
Entrez gene summary
This intronless gene encodes a member of the SRY-related HMG-box (SOX) family of transcription factors involved in the regulation of embryonic development and in the determination of cell fate. The product of this gene is required for stem-cell maintenance in the central nervous system, and also regulates gene expression in the stomach. Mutations in this gene have been associated with optic nerve hypoplasia and with syndromic microphthalmia, a severe form of structural eye malformation. This gene lies within an intron of another gene called SOX2 overlapping transcript (SOX2OT). [provided by RefSeq, Jul 2008]
The protein browser displays the antigen location on the target protein(s) and the features of the target protein. The tabs at the top of the protein view section can be used to switch between the different splice variants to which an antigen has been mapped.
At the top of the view, the position of the antigen (identified by the corresponding HPA identifier) is shown as a green bar. A yellow triangle on the bar indicates a <100% sequence identity to the protein target.
Under the antigens, the maximum percent sequence identity of the protein to all other proteins from other human genes is displayed, using a sliding window of 10 aa residues (HsID 10) or 50 aa residues (HsID 50) (read more).
If a signal peptide is predicted by a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius (turquoise) and/or transmembrane regions (orange) are predicted by MDM, these are displayed.
Low complexity regions are shown in yellow and InterPro regions in green. Common (purple) and unique (grey) regions between different splice variants of the gene are also displayed (read more), and at the bottom of the protein view is the protein scale.
SOX2-001
PROTEIN INFORMATIONi
The protein information section displays alternative protein-coding transcripts (splice variants) encoded by this gene according to the Ensembl database.
The ENSP identifier links to the Ensembl website protein summary, while the ENST identifier links to the Ensembl website transcript summary for the selected splice variant. The data in the UniProt column can be expanded to show links to all matching UniProt identifiers for this protein.
The protein classes assigned to this protein are shown if expanding the data in the protein class column. Parent protein classes are in bold font and subclasses are listed under the parent class.
The Gene Ontology terms assigned to this protein are listed if expanding the Gene ontology column. The length of the protein (amino acid residues according to Ensembl), molecular mass (kDalton), predicted signal peptide (according to a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius) and the number of predicted transmembrane region(s) (according to MDM) are also reported.
Predicted intracellular proteins Transcription factors Other all-alpha-helical DNA-binding domains Cancer-related genes COSMIC somatic mutations in cancer genes COSMIC Amplifications COSMIC Somatic Mutations Disease related genes Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000122 [negative regulation of transcription from RNA polymerase II promoter] GO:0000976 [transcription regulatory region sequence-specific DNA binding] GO:0000981 [RNA polymerase II transcription factor activity, sequence-specific DNA binding] GO:0001077 [transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding] GO:0001649 [osteoblast differentiation] GO:0001654 [eye development] GO:0001708 [cell fate specification] GO:0001714 [endodermal cell fate specification] GO:0002052 [positive regulation of neuroblast proliferation] GO:0003677 [DNA binding] GO:0003682 [chromatin binding] GO:0003700 [transcription factor activity, sequence-specific DNA binding] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005654 [nucleoplasm] GO:0005667 [transcription factor complex] GO:0005737 [cytoplasm] GO:0005829 [cytosol] GO:0006325 [chromatin organization] GO:0006355 [regulation of transcription, DNA-templated] GO:0006357 [regulation of transcription from RNA polymerase II promoter] GO:0006366 [transcription from RNA polymerase II promoter] GO:0007050 [cell cycle arrest] GO:0007605 [sensory perception of sound] GO:0009611 [response to wounding] GO:0010033 [response to organic substance] GO:0010468 [regulation of gene expression] GO:0019827 [stem cell population maintenance] GO:0021781 [glial cell fate commitment] GO:0021879 [forebrain neuron differentiation] GO:0021983 [pituitary gland development] GO:0021984 [adenohypophysis development] GO:0021987 [cerebral cortex development] GO:0022409 [positive regulation of cell-cell adhesion] GO:0030178 [negative regulation of Wnt signaling pathway] GO:0030539 [male genitalia development] GO:0030858 [positive regulation of epithelial cell differentiation] GO:0030900 [forebrain development] GO:0030910 [olfactory placode formation] GO:0031490 [chromatin DNA binding] GO:0032526 [response to retinoic acid] GO:0035019 [somatic stem cell population maintenance] GO:0035198 [miRNA binding] GO:0042246 [tissue regeneration] GO:0042472 [inner ear morphogenesis] GO:0043281 [regulation of cysteine-type endopeptidase activity involved in apoptotic process] GO:0043410 [positive regulation of MAPK cascade] GO:0043565 [sequence-specific DNA binding] GO:0043586 [tongue development] GO:0044212 [transcription regulatory region DNA binding] GO:0044798 [nuclear transcription factor complex] GO:0045165 [cell fate commitment] GO:0045596 [negative regulation of cell differentiation] GO:0045597 [positive regulation of cell differentiation] GO:0045665 [negative regulation of neuron differentiation] GO:0045666 [positive regulation of neuron differentiation] GO:0045668 [negative regulation of osteoblast differentiation] GO:0045747 [positive regulation of Notch signaling pathway] GO:0045893 [positive regulation of transcription, DNA-templated] GO:0045944 [positive regulation of transcription from RNA polymerase II promoter] GO:0046148 [pigment biosynthetic process] GO:0046982 [protein heterodimerization activity] GO:0048286 [lung alveolus development] GO:0048568 [embryonic organ development] GO:0048646 [anatomical structure formation involved in morphogenesis] GO:0048663 [neuron fate commitment] GO:0048839 [inner ear development] GO:0048852 [diencephalon morphogenesis] GO:0048863 [stem cell differentiation] GO:0050680 [negative regulation of epithelial cell proliferation] GO:0050767 [regulation of neurogenesis] GO:0050910 [detection of mechanical stimulus involved in sensory perception of sound] GO:0050973 [detection of mechanical stimulus involved in equilibrioception] GO:0060042 [retina morphogenesis in camera-type eye] GO:0060235 [lens induction in camera-type eye] GO:0060441 [epithelial tube branching involved in lung morphogenesis] GO:0070848 [response to growth factor] GO:0090090 [negative regulation of canonical Wnt signaling pathway] GO:0097150 [neuronal stem cell population maintenance]
