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.
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
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 knowledge-based expression profile.
Antibody staining mainly consistent with RNA expression data.
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.
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 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.
RNA tissue category: Mixed
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.
RNA tissue category: Mixed
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.
RNA tissue category: Mixed
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.
SOX9 (HGNC Symbol)
CMD1, CMPD1, SRA1
SRY (sex determining region Y)-box 9 (HGNC Symbol)
Entrez gene summary
The protein encoded by this gene recognizes the sequence CCTTGAG along with other members of the HMG-box class DNA-binding proteins. It acts during chondrocyte differentiation and, with steroidogenic factor 1, regulates transcription of the anti-Muellerian hormone (AMH) gene. Deficiencies lead to the skeletal malformation syndrome campomelic dysplasia, frequently with sex reversal. [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.
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 Candidate cancer biomarkers Disease related genes Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
GO:0000976 [transcription regulatory region sequence-specific DNA binding] GO:0000981 [RNA polymerase II transcription factor activity, sequence-specific DNA binding] GO:0001046 [core promoter sequence-specific DNA binding] GO:0001077 [transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding] GO:0001158 [enhancer sequence-specific DNA binding] GO:0001228 [transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding] GO:0001501 [skeletal system development] GO:0001502 [cartilage condensation] GO:0001503 [ossification] GO:0001658 [branching involved in ureteric bud morphogenesis] GO:0001708 [cell fate specification] GO:0001837 [epithelial to mesenchymal transition] GO:0001894 [tissue homeostasis] GO:0001934 [positive regulation of protein phosphorylation] GO:0001942 [hair follicle development] GO:0002053 [positive regulation of mesenchymal cell proliferation] GO:0002062 [chondrocyte differentiation] GO:0002063 [chondrocyte development] GO:0002683 [negative regulation of immune system process] GO:0003170 [heart valve development] GO:0003179 [heart valve morphogenesis] GO:0003188 [heart valve formation] GO:0003203 [endocardial cushion morphogenesis] GO:0003413 [chondrocyte differentiation involved in endochondral bone morphogenesis] GO:0003415 [chondrocyte hypertrophy] GO:0003677 [DNA binding] GO:0003682 [chromatin binding] GO:0003700 [transcription factor activity, sequence-specific DNA binding] GO:0003705 [transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding] GO:0004672 [protein kinase activity] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005654 [nucleoplasm] GO:0005667 [transcription factor complex] GO:0006334 [nucleosome assembly] GO:0006338 [chromatin remodeling] GO:0006357 [regulation of transcription from RNA polymerase II promoter] GO:0006366 [transcription from RNA polymerase II promoter] GO:0006461 [protein complex assembly] GO:0007010 [cytoskeleton organization] GO:0007165 [signal transduction] GO:0007173 [epidermal growth factor receptor signaling pathway] GO:0007219 [Notch signaling pathway] GO:0007283 [spermatogenesis] GO:0007417 [central nervous system development] GO:0007507 [heart development] GO:0008013 [beta-catenin binding] GO:0008284 [positive regulation of cell proliferation] GO:0008285 [negative regulation of cell proliferation] GO:0008584 [male gonad development] GO:0010564 [regulation of cell cycle process] GO:0010628 [positive regulation of gene expression] GO:0010629 [negative regulation of gene expression] GO:0010634 [positive regulation of epithelial cell migration] GO:0014032 [neural crest cell development] GO:0014068 [positive regulation of phosphatidylinositol 3-kinase signaling] GO:0016337 [single organismal cell-cell adhesion] GO:0019100 [male germ-line sex determination] GO:0019933 [cAMP-mediated signaling] GO:0030154 [cell differentiation] GO:0030155 [regulation of cell adhesion] GO:0030198 [extracellular matrix organization] GO:0030238 [male sex determination] GO:0030279 [negative regulation of ossification] GO:0030502 [negative regulation of bone mineralization] GO:0030850 [prostate gland development] GO:0030857 [negative regulation of epithelial cell differentiation] GO:0030858 [positive regulation of epithelial cell differentiation] GO:0030879 [mammary gland development] GO:0030903 [notochord development] GO:0030916 [otic vesicle formation] GO:0031018 [endocrine pancreas development] GO:0032331 [negative regulation of chondrocyte differentiation] GO:0032332 [positive regulation of chondrocyte differentiation] GO:0032808 [lacrimal gland development] GO:0034236 [protein kinase A catalytic subunit binding] GO:0034504 [protein localization to nucleus] GO:0035019 [somatic stem cell population maintenance] GO:0035326 [enhancer binding] GO:0035622 [intrahepatic bile duct development] GO:0042127 [regulation of cell proliferation] GO:0042981 [regulation of apoptotic process] GO:0043066 [negative regulation of apoptotic process] GO:0043234 [protein complex] GO:0043425 [bHLH transcription factor binding] GO:0043491 [protein kinase B signaling] GO:0043565 [sequence-specific DNA binding] GO:0044212 [transcription regulatory region DNA binding] GO:0044798 [nuclear transcription factor complex] GO:0045165 [cell fate commitment] GO:0045595 [regulation of cell differentiation] GO:0045662 [negative regulation of myoblast differentiation] GO:0045732 [positive regulation of protein catabolic process] GO:0045892 [negative regulation of transcription, DNA-templated] GO:0045893 [positive regulation of transcription, DNA-templated] GO:0045944 [positive regulation of transcription from RNA polymerase II promoter] GO:0046533 [negative regulation of photoreceptor cell differentiation] GO:0046982 [protein heterodimerization activity] GO:0048709 [oligodendrocyte differentiation] GO:0048873 [homeostasis of number of cells within a tissue] GO:0050679 [positive regulation of epithelial cell proliferation] GO:0050680 [negative regulation of epithelial cell proliferation] GO:0051216 [cartilage development] GO:0060008 [Sertoli cell differentiation] GO:0060009 [Sertoli cell development] GO:0060018 [astrocyte fate commitment] GO:0060041 [retina development in camera-type eye] GO:0060174 [limb bud formation] GO:0060221 [retinal rod cell differentiation] GO:0060350 [endochondral bone morphogenesis] GO:0060441 [epithelial tube branching involved in lung morphogenesis] GO:0060487 [lung epithelial cell differentiation] GO:0060512 [prostate gland morphogenesis] GO:0060517 [epithelial cell proliferation involved in prostatic bud elongation] GO:0060532 [bronchus cartilage development] GO:0060534 [trachea cartilage development] GO:0060729 [intestinal epithelial structure maintenance] GO:0060784 [regulation of cell proliferation involved in tissue homeostasis] GO:0061036 [positive regulation of cartilage development] GO:0061046 [regulation of branching involved in lung morphogenesis] GO:0061138 [morphogenesis of a branching epithelium] GO:0061145 [lung smooth muscle development] GO:0070168 [negative regulation of biomineral tissue development] GO:0070371 [ERK1 and ERK2 cascade] GO:0070384 [Harderian gland development] GO:0071260 [cellular response to mechanical stimulus] GO:0071300 [cellular response to retinoic acid] GO:0071347 [cellular response to interleukin-1] GO:0071364 [cellular response to epidermal growth factor stimulus] GO:0071504 [cellular response to heparin] GO:0071560 [cellular response to transforming growth factor beta stimulus] GO:0071599 [otic vesicle development] GO:0072034 [renal vesicle induction] GO:0072170 [metanephric tubule development] GO:0072189 [ureter development] GO:0072190 [ureter urothelium development] GO:0072193 [ureter smooth muscle cell differentiation] GO:0072197 [ureter morphogenesis] GO:0072289 [metanephric nephron tubule formation] GO:0090090 [negative regulation of canonical Wnt signaling pathway] GO:0090103 [cochlea morphogenesis] GO:0090184 [positive regulation of kidney development] GO:0090190 [positive regulation of branching involved in ureteric bud morphogenesis] GO:0097157 [pre-mRNA intronic binding] GO:1901203 [positive regulation of extracellular matrix assembly] GO:2000020 [positive regulation of male gonad development] GO:2000138 [positive regulation of cell proliferation involved in heart morphogenesis] GO:2000741 [positive regulation of mesenchymal stem cell differentiation] GO:2000794 [regulation of epithelial cell proliferation involved in lung morphogenesis] GO:2001054 [negative regulation of mesenchymal cell apoptotic process]