Name | Number of supported studies  | Average coverage | |
|---|---|---|---|
| astrocyte | 18 studies | 34% ± 14% | |
| epithelial cell | 8 studies | 29% ± 9% | |
| Mueller cell | 5 studies | 32% ± 13% | |
| abnormal cell | 4 studies | 28% ± 13% | |
| basal cell | 4 studies | 29% ± 7% | |
| brush cell | 4 studies | 54% ± 18% | |
| intestinal crypt stem cell | 4 studies | 26% ± 7% | |
| duct epithelial cell | 3 studies | 17% ± 0% | |
| retinal pigment epithelial cell | 3 studies | 40% ± 17% | |
| ependymal cell | 3 studies | 41% ± 11% | |
| goblet cell | 3 studies | 30% ± 11% |
Insufficient scRNA-seq data for expression of SOX9 at tissue level.
Tissue | GTEx Coverage | GTEx Average TPM | GTEx Number of samples | TCGA Coverage | TCGA Average TPM | TCGA Number of samples |
|---|---|---|---|---|---|---|
| brain | 98% | 4953.96 | 2594 / 2642 | 99% | 208.35 | 698 / 705 |
| prostate | 96% | 3289.86 | 236 / 245 | 97% | 115.29 | 487 / 502 |
| pancreas | 100% | 3167.92 | 327 / 328 | 91% | 103.06 | 162 / 178 |
| thymus | 98% | 2197.71 | 640 / 653 | 80% | 52.38 | 483 / 605 |
| stomach | 74% | 2154.66 | 264 / 359 | 98% | 203.33 | 281 / 286 |
| breast | 68% | 2667.44 | 311 / 459 | 87% | 98.74 | 975 / 1118 |
| kidney | 78% | 2098.21 | 69 / 89 | 72% | 77.35 | 651 / 901 |
| intestine | 45% | 1261.38 | 435 / 966 | 99% | 218.61 | 521 / 527 |
| esophagus | 38% | 852.98 | 551 / 1445 | 94% | 186.29 | 172 / 183 |
| skin | 69% | 2990.80 | 1255 / 1809 | 33% | 26.50 | 154 / 472 |
| lung | 42% | 488.51 | 242 / 578 | 56% | 55.40 | 652 / 1155 |
| heart | 91% | 1723.36 | 783 / 861 | 0% | 0 | 0 / 0 |
| ovary | 1% | 10.27 | 2 / 180 | 85% | 69.65 | 364 / 430 |
| uterus | 7% | 80.62 | 12 / 170 | 68% | 58.81 | 312 / 459 |
| bladder | 10% | 102.52 | 2 / 21 | 56% | 72.34 | 284 / 504 |
| tonsil | 0% | 0 | 0 / 0 | 62% | 37.06 | 28 / 45 |
| liver | 7% | 66.30 | 16 / 226 | 41% | 35.93 | 166 / 406 |
| adrenal gland | 21% | 186.72 | 54 / 258 | 23% | 15.43 | 54 / 230 |
| blood vessel | 40% | 494.84 | 529 / 1335 | 0% | 0 | 0 / 0 |
| adipose | 32% | 353.05 | 386 / 1204 | 0% | 0 | 0 / 0 |
| eye | 0% | 0 | 0 / 0 | 23% | 9.90 | 18 / 80 |
| peripheral blood | 18% | 701.12 | 164 / 929 | 0% | 0 | 0 / 0 |
| muscle | 6% | 54.90 | 48 / 803 | 0% | 0 | 0 / 0 |
| lymph node | 0% | 0 | 0 / 0 | 3% | 0.82 | 1 / 29 |
| abdomen | 0% | 0 | 0 / 0 | 0% | 0 | 0 / 0 |
| bone marrow | 0% | 0 | 0 / 0 | 0% | 0 | 0 / 0 |
| diaphragm | 0% | 0 | 0 / 0 | 0% | 0 | 0 / 0 |
| gingiva | 0% | 0 | 0 / 0 | 0% | 0 | 0 / 0 |
| nasal cavity | 0% | 0 | 0 / 0 | 0% | 0 | 0 / 0 |
| nasopharynx | 0% | 0 | 0 / 0 | 0% | 0 | 0 / 0 |
| nose | 0% | 0 | 0 / 0 | 0% | 0 | 0 / 0 |
| placenta | 0% | 0 | 0 / 0 | 0% | 0 | 0 / 0 |
| spinal column | 0% | 0 | 0 / 0 | 0% | 0 | 0 / 0 |
| spleen | 0% | 0 | 0 / 241 | 0% | 0 | 0 / 0 |
| ureter | 0% | 0 | 0 / 0 | 0% | 0 | 0 / 1 |
| GO_0006366 | Biological process | transcription by RNA polymerase II |
| GO_0001658 | Biological process | branching involved in ureteric bud morphogenesis |
| GO_0071560 | Biological process | cellular response to transforming growth factor beta stimulus |
| GO_0071260 | Biological process | cellular response to mechanical stimulus |
| GO_0030916 | Biological process | otic vesicle formation |
| GO_0071364 | Biological process | cellular response to epidermal growth factor stimulus |
| GO_0045662 | Biological process | negative regulation of myoblast differentiation |
| GO_0032808 | Biological process | lacrimal gland development |
| GO_0002062 | Biological process | chondrocyte differentiation |
| GO_0060441 | Biological process | epithelial tube branching involved in lung morphogenesis |
| GO_0030850 | Biological process | prostate gland development |
| GO_0060534 | Biological process | trachea cartilage development |
| GO_0003203 | Biological process | endocardial cushion morphogenesis |
| GO_0097152 | Biological process | mesenchymal cell apoptotic process |
| GO_0090090 | Biological process | negative regulation of canonical Wnt signaling pathway |
| GO_0006334 | Biological process | nucleosome assembly |
| GO_0032331 | Biological process | negative regulation of chondrocyte differentiation |
| GO_0002053 | Biological process | positive regulation of mesenchymal cell proliferation |
| GO_0030857 | Biological process | negative regulation of epithelial cell differentiation |
| GO_0070168 | Biological process | negative regulation of biomineral tissue development |
| GO_0043066 | Biological process | negative regulation of apoptotic process |
| GO_0072289 | Biological process | metanephric nephron tubule formation |
| GO_2000020 | Biological process | positive regulation of male gonad development |
| GO_0043491 | Biological process | phosphatidylinositol 3-kinase/protein kinase B signal transduction |
| GO_0007173 | Biological process | epidermal growth factor receptor signaling pathway |
| GO_0001501 | Biological process | skeletal system development |
| GO_0051897 | Biological process | positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction |
| GO_0014036 | Biological process | neural crest cell fate specification |
| GO_0030903 | Biological process | notochord development |
| GO_0035622 | Biological process | intrahepatic bile duct development |
| GO_0030858 | Biological process | positive regulation of epithelial cell differentiation |
| GO_0060532 | Biological process | bronchus cartilage development |
| GO_0030279 | Biological process | negative regulation of ossification |
| GO_0071300 | Biological process | cellular response to retinoic acid |
| GO_0072089 | Biological process | stem cell proliferation |
| GO_0030879 | Biological process | mammary gland development |
| GO_0003430 | Biological process | growth plate cartilage chondrocyte growth |
| GO_0007219 | Biological process | Notch signaling pathway |
| GO_0071773 | Biological process | cellular response to BMP stimulus |
| GO_0070542 | Biological process | response to fatty acid |
| GO_0060009 | Biological process | Sertoli cell development |
| GO_0003415 | Biological process | chondrocyte hypertrophy |
| GO_0010629 | Biological process | negative regulation of gene expression |
| GO_0085029 | Biological process | extracellular matrix assembly |
| GO_0060221 | Biological process | retinal rod cell differentiation |
| GO_0007165 | Biological process | signal transduction |
| GO_1902894 | Biological process | negative regulation of miRNA transcription |
| GO_0010628 | Biological process | positive regulation of gene expression |
| GO_0048665 | Biological process | neuron fate specification |
| GO_0019933 | Biological process | cAMP-mediated signaling |
| GO_0071347 | Biological process | cellular response to interleukin-1 |
| GO_2000741 | Biological process | positive regulation of mesenchymal stem cell differentiation |
| GO_0060008 | Biological process | Sertoli cell differentiation |
| GO_1901203 | Biological process | positive regulation of extracellular matrix assembly |
| GO_0060509 | Biological process | type I pneumocyte differentiation |
| GO_0045732 | Biological process | positive regulation of protein catabolic process |
| GO_0050679 | Biological process | positive regulation of epithelial cell proliferation |
| GO_0060517 | Biological process | epithelial cell proliferation involved in prostatic bud elongation |
| GO_0070371 | Biological process | ERK1 and ERK2 cascade |
| GO_0042981 | Biological process | regulation of apoptotic process |
| GO_2000138 | Biological process | positive regulation of cell proliferation involved in heart morphogenesis |
| GO_0010463 | Biological process | mesenchymal cell proliferation |
| GO_0001894 | Biological process | tissue homeostasis |
| GO_0072197 | Biological process | ureter morphogenesis |
| GO_0060729 | Biological process | intestinal epithelial structure maintenance |
| GO_0051216 | Biological process | cartilage development |
| GO_0003413 | Biological process | chondrocyte differentiation involved in endochondral bone morphogenesis |
| GO_0001708 | Biological process | cell fate specification |
| GO_0002009 | Biological process | morphogenesis of an epithelium |
| GO_0003188 | Biological process | heart valve formation |
| GO_0003179 | Biological process | heart valve morphogenesis |
| GO_0032332 | Biological process | positive regulation of chondrocyte differentiation |
| GO_0003180 | Biological process | aortic valve morphogenesis |
| GO_0007010 | Biological process | cytoskeleton organization |
| GO_0001934 | Biological process | positive regulation of protein phosphorylation |
| GO_0060174 | Biological process | limb bud formation |
| GO_0061046 | Biological process | regulation of branching involved in lung morphogenesis |
| GO_0061145 | Biological process | lung smooth muscle development |
| GO_0045893 | Biological process | positive regulation of DNA-templated transcription |
| GO_1902732 | Biological process | positive regulation of chondrocyte proliferation |
| GO_0010564 | Biological process | regulation of cell cycle process |
| GO_0030502 | Biological process | negative regulation of bone mineralization |
| GO_0045668 | Biological process | negative regulation of osteoblast differentiation |
| GO_0090190 | Biological process | positive regulation of branching involved in ureteric bud morphogenesis |
| GO_0070384 | Biological process | Harderian gland development |
| GO_0008584 | Biological process | male gonad development |
| GO_0072193 | Biological process | ureter smooth muscle cell differentiation |
| GO_0008284 | Biological process | positive regulation of cell population proliferation |
| GO_0060575 | Biological process | intestinal epithelial cell differentiation |
| GO_0001502 | Biological process | cartilage condensation |
| GO_2001054 | Biological process | negative regulation of mesenchymal cell apoptotic process |
| GO_0045892 | Biological process | negative regulation of DNA-templated transcription |
| GO_0042127 | Biological process | regulation of cell population proliferation |
| GO_0010634 | Biological process | positive regulation of epithelial cell migration |
| GO_0061036 | Biological process | positive regulation of cartilage development |
| GO_0061138 | Biological process | morphogenesis of a branching epithelium |
| GO_0045944 | Biological process | positive regulation of transcription by RNA polymerase II |
| GO_0035019 | Biological process | somatic stem cell population maintenance |
| GO_0001837 | Biological process | epithelial to mesenchymal transition |
| GO_0007283 | Biological process | spermatogenesis |
| GO_0072190 | Biological process | ureter urothelium development |
| GO_0061323 | Biological process | cell proliferation involved in heart morphogenesis |
| GO_0097065 | Biological process | anterior head development |
| GO_0007507 | Biological process | heart development |
| GO_0071504 | Biological process | cellular response to heparin |
| GO_0060784 | Biological process | regulation of cell proliferation involved in tissue homeostasis |
| GO_0014070 | Biological process | response to organic cyclic compound |
| GO_2000648 | Biological process | positive regulation of stem cell proliferation |
| GO_0060041 | Biological process | retina development in camera-type eye |
| GO_0090103 | Biological process | cochlea morphogenesis |
| GO_0000122 | Biological process | negative regulation of transcription by RNA polymerase II |
| GO_0006338 | Biological process | chromatin remodeling |
| GO_0050680 | Biological process | negative regulation of epithelial cell proliferation |
| GO_0014032 | Biological process | neural crest cell development |
| GO_0060070 | Biological process | canonical Wnt signaling pathway |
| GO_0065003 | Biological process | protein-containing complex assembly |
| GO_0046533 | Biological process | negative regulation of photoreceptor cell differentiation |
| GO_0072034 | Biological process | renal vesicle induction |
| GO_2000794 | Biological process | regulation of epithelial cell proliferation involved in lung morphogenesis |
| GO_0003170 | Biological process | heart valve development |
| GO_0002067 | Biological process | glandular epithelial cell differentiation |
| GO_0034504 | Biological process | protein localization to nucleus |
| GO_0046322 | Biological process | negative regulation of fatty acid oxidation |
| GO_0030282 | Biological process | bone mineralization |
| GO_0002683 | Biological process | negative regulation of immune system process |
| GO_0001942 | Biological process | hair follicle development |
| GO_0019100 | Biological process | male germ-line sex determination |
| GO_0048709 | Biological process | oligodendrocyte differentiation |
| GO_0060018 | Biological process | astrocyte fate commitment |
| GO_1904864 | Biological process | negative regulation of beta-catenin-TCF complex assembly |
| GO_0021780 | Biological process | glial cell fate specification |
| GO_0031018 | Biological process | endocrine pancreas development |
| GO_0030155 | Biological process | regulation of cell adhesion |
| GO_0098609 | Biological process | cell-cell adhesion |
| GO_0090184 | Biological process | positive regulation of kidney development |
| GO_0005634 | Cellular component | nucleus |
| GO_0005654 | Cellular component | nucleoplasm |
| GO_0032991 | Cellular component | protein-containing complex |
| GO_0000785 | Cellular component | chromatin |
| GO_0005667 | Cellular component | transcription regulator complex |
| GO_0001228 | Molecular function | DNA-binding transcription activator activity, RNA polymerase II-specific |
| GO_0034236 | Molecular function | protein kinase A catalytic subunit binding |
| GO_0000978 | Molecular function | RNA polymerase II cis-regulatory region sequence-specific DNA binding |
| GO_0043565 | Molecular function | sequence-specific DNA binding |
| GO_0003682 | Molecular function | chromatin binding |
| GO_0000987 | Molecular function | cis-regulatory region sequence-specific DNA binding |
| GO_0097157 | Molecular function | pre-mRNA intronic binding |
| GO_0003700 | Molecular function | DNA-binding transcription factor activity |
| GO_0005515 | Molecular function | protein binding |
| GO_0043425 | Molecular function | bHLH transcription factor binding |
| GO_0000981 | Molecular function | DNA-binding transcription factor activity, RNA polymerase II-specific |
| GO_1990837 | Molecular function | sequence-specific double-stranded DNA binding |
| GO_0008013 | Molecular function | beta-catenin binding |
| Gene name | SOX9 |
| Protein name | Transcription factor SOX-9 SRY (Sex determining region Y)-box9 SRY-box 9 Transcription factor |
| Synonyms | |
| Description | FUNCTION: Transcription factor that plays a key role in chondrocytes differentiation and skeletal development . Specifically binds the 5'-ACAAAG-3' DNA motif present in enhancers and super-enhancers and promotes expression of genes important for chondrogenesis, including cartilage matrix protein-coding genes COL2A1, COL4A2, COL9A1, COL11A2 and ACAN, SOX5 and SOX6 . Also binds to some promoter regions (By similarity). Plays a central role in successive steps of chondrocyte differentiation (By similarity). Absolutely required for precartilaginous condensation, the first step in chondrogenesis during which skeletal progenitors differentiate into prechondrocytes (By similarity). Together with SOX5 and SOX6, required for overt chondrogenesis when condensed prechondrocytes differentiate into early stage chondrocytes, the second step in chondrogenesis (By similarity). Later, required to direct hypertrophic maturation and block osteoblast differentiation of growth plate chondrocytes: maintains chondrocyte columnar proliferation, delays prehypertrophy and then prevents osteoblastic differentiation of chondrocytes by lowering beta-catenin (CTNNB1) signaling and RUNX2 expression (By similarity). Also required for chondrocyte hypertrophy, both indirectly, by keeping the lineage fate of chondrocytes, and directly, by remaining present in upper hypertrophic cells and transactivating COL10A1 along with MEF2C (By similarity). Low lipid levels are the main nutritional determinant for chondrogenic commitment of skeletal progenitor cells: when lipids levels are low, FOXO (FOXO1 and FOXO3) transcription factors promote expression of SOX9, which induces chondrogenic commitment and suppresses fatty acid oxidation (By similarity). Mechanistically, helps, but is not required, to remove epigenetic signatures of transcriptional repression and deposit active promoter and enhancer marks at chondrocyte-specific genes (By similarity). Acts in cooperation with the Hedgehog pathway-dependent GLI (GLI1 and GLI3) transcription factors (By similarity). In addition to cartilage development, also acts as a regulator of proliferation and differentiation in epithelial stem/progenitor cells: involved in the lung epithelium during branching morphogenesis, by balancing proliferation and differentiation and regulating the extracellular matrix (By similarity). Controls epithelial branching during kidney development (By similarity). . |
| Accessions | U5XK44 P48436 ENST00000245479.3 A0A0U4U3E8 U5XJZ4 U5XKW5 U5XN67 U5XJZ1 U5XMM4 A0A0U4YWA5 U5XKW9 S6CBB2 U5XN63 U5XK50 U5XJY7 |
