The cancer tissue page shows antibody staining in 20 different cancers. The assay and annotation is described here.
This page starts with information about the protein evidence and, when applicable, also protein class. Below the summary, a selection of four standard cancer tissue samples is displayed as representative of the overall staining pattern. From left: colorectal cancer, breast cancer, prostate cancer and lung cancer. An additional 5th image can be added as a complement.
Cancer-related genes, Disease related genes, Predicted intracellular proteins, Transcription factors
Evidence at protein level
The cancer tissue summary page shows antibody staining in 20 different cancers. The assay and annotation is described here.
For each cancer, the fraction of samples with antibody staining/protein expression level high, medium, low, or not detected are provided by the blue-scale color-coding (as described by the color-coding scale in the box to the right). The length of the bar represents the number of patient samples analyzed (max=12 patients). 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. The tooltip function displays additional data for the features in the staining summary view.
Next to the cancer staining data, the protein expression data of normal tissues or specific cell types corresponding to each cancer are shown and protein expression levels are indicated by the blue-scale color coding.
At the bottom of the page, a summary of the overall protein expression pattern across the analyzed cancer tissues as well as information about literature conformity are presented.
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 (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]