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.
TCGA (cancer tissue):
Expressed in all
HPA (cell line):
Cell line enhanced (AN3-CA, Hep G2, U-251 MG)
HPA (normal tissue):
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 expression normal tissuei
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 - normal tissuesi
Reliability score (score description), divided into Enhanced, Supported, Approved, or Uncertain, is evaluated in normal tissues and based on consistency between antibody staining pattern, available RNA-Seq and gene/protein characterization data, as well as similarity between independent antibodies targeting the same protein.
Kaplan-Meier plots for all cancers where high expression of this gene has significant (p<0.001) association with patient survival are shown in this summary. Whether the prognosis is favourable or unfavourable is indicated in brackets. Each Kaplan-Meier plot is clickable and redirects to a detailed page that includes individual expression and survival data for patients with the selected cancer.
RNA expression overview shows RNA-seq data from The Cancer Genome Atlas (TCGA).
RNA-seq data in 17 cancer types are reported as median FPKM (number Fragments Per Kilobase of exon per Million reads), generated by the The Cancer Genome Atlas (TCGA). RNA cancer tissue category is calculated based on mRNA expression levels across all 17 cancer tissues and include: cancer tissue enriched, cancer group enriched, cancer tissue enhanced, expressed in all, mixed and not detected. To access cancer specific RNA and prognostic data, click on the cancer name. The cancer types are color-coded according to which type of normal organ the cancer originates from.
Antibody staining in 20 different cancers is summarized by a selection of four standard cancer tissue samples representative of the overall staining pattern. From left: colorectal cancer, breast cancer, prostate cancer and lung cancer. An additional fifth image can be added as a complement. The assay and annotation is described here. Note that samples used for immunohistochemistry by the Human Protein Atlas do not correspond to samples in the TCGA dataset.
For each cancer, color-coded bars indicate the percentage of patients (maximum 12 patients) with high and medium protein expression level. The cancer types are color-coded according to which type of normal organ the cancer originates from. Low or not detected protein expression results in a white bar. Mouse-over function shows details about expression level and normal tissue of origin. The images and annotations can be accessed by clicking on the cancer name or protein expression bar. If more than one antibody is analyzed, the tabs at the top of the staining summary section can be used to toggle between the different antibodies.
Gliomas and colorectal cancers showed moderate to strong nuclear immunoreactivity. Breast, stomach, pancreas cancers along with several cervical, ovarian, lung, skin and few urothelial cancers displayed moderate nuclear positivity. Other cancer tissues were in general weakly stained or were negative.
Moderate to strong nuclear immunoreactivity was exhibited in most cancer tissues. Additional/or cytoplasmic positivity was observed in few endometrial, lung and prostate cancers. Lymphomas along with several hepatocellular carcinomas and testicular cancers were negative.
Most cancer tissues showed moderate to strong nuclear positivity in varying fractions of tumor cells. Lymphomas were negative.
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-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). The region with the lowest possible identity is always selected for antigen design, with a maximum identity of 60% allowed for designing a single-target antigen (read more).
The curve in blue displays the predicted antigenicity i.e. the tendency for different regions of the protein to generate an immune response, with peak regions being predicted to be more antigenic.The curve shows average values based on a sliding window approach using an in-house propensity scale. (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: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: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:0006351 [transcription, DNA-templated] 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: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:1902894 [negative regulation of pri-miRNA transcription from RNA polymerase II promoter] 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]