TF information
| TF name: | VDR |
| TF family: | THR-like |
| Ensembl gene ID: | ENSG00000111424 |
| Ensembl protein ID: | ENSP00000229022, ENSP00000449074, ENSP00000449573, ENSP00000447173, ENSP00000448659, ENSP00000450105, ENSP00000378734, ENSP00000449561 |
| Entrez gene ID: | 7421 |
| Database name | Link | Database name | Link |
| NCBI Gene: |  |
Genecards: |  |
| Uniprot: |  |
Wikipedia: |  |
| Cosmic 3D: |  |
Geneontology: |  |
| CCLE: |  |
Frequency of VDR in all biosamples
| Sample ID | Biosample type | Tissue type | Biosample name | TF Frequency |
|---|---|---|---|---|
| Sample_02_236 | Cell line | Colon | V206 | 0.19875776397516 |
| Sample_02_237 | Cell line | Colon | V389 | 0.4701638137309 |
| Sample_02_241 | Cell line | Colon | V456 | 1 |
| Sample_02_358 | Cell line | Colon | LS180 | 0.40916271721959 |
VDR distribution in samples’ most representative CRC
| Sample ID | Tissue type | Biosample type | Biosample name |
|---|---|---|---|
| Sample_02_241 | Colon | Cell line | V456 |
| Sample_02_358 | Colon | Cell line | LS180 |
VDR distribution in all CRCs
Genomic distribution of SEs associated with VDR
Genomic distribution of SEs associated with TF
Figure legend:
Genomic distribution of SEs associated with TF: It can roughly understand the genomic regions of SEs associated with TF, and help to carry out the next analysis, such as knocking down the experiment.
What is important information?
The yellow box can be thought of as the common genomic regions that regulates the SEs associated with TF. For example, if a knockdown experiment is performed on this region, then theoretically, the expression of the TF will be greatly reduced.
| Database name | Link |
|---|---|
| Cosmic: |  |
| Cosmic cell lines: |  |
| Depmap: |  |
TCGA somatic mutations and clinical variants of VDR
| rsID | Chr | Start | Stop | Ref | Alt | Gene_region | Gene_symble | Effect | TCGA_Occurrence |
|---|---|---|---|---|---|---|---|---|---|
| - | chr12 | 48240500 | 48240500 | C | G | exonic | VDR | nonsynonymous | SKCM|1|368|0.00272 |
| rs776080166 | chr12 | 48251326 | 48251326 | C | T | exonic | VDR | synonymous | SKCM|1|368|0.00272 |
| - | chr12 | 48251385 | 48251385 | G | A | exonic | VDR | nonsynonymous | PRAD|1|499|0.00200 |
| - | chr12 | 48258873 | 48258873 | G | A | exonic | VDR | synonymous | COAD|1|367|0.00272,COADREAD|1|489|0.00204 |
| - | chr12 | 48238538 | 48238538 | C | T | exonic | VDR | synonymous | HNSC|1|512|0.00195 |
| - | chr12 | 48251312 | 48251312 | G | A | exonic | VDR | nonsynonymous | COAD|1|367|0.00272,COADREAD|1|489|0.00204 |
| - | chr12 | 48272869 | 48272869 | G | A | exonic | VDR | synonymous | STAD|2|395|0.00506,STES|2|395|0.00506 |
| - | chr12 | 48250947 | 48250947 | G | A | exonic | VDR | nonsynonymous | SKCM|1|368|0.00272 |
| - | chr12 | 48258951 | 48258951 | C | T | exonic | VDR | nonsynonymous | LUAD|1|543|0.00184 |
| - | chr12 | 48240119 | 48240119 | T | A | exonic | VDR | synonymous | LUAD|1|543|0.00184 |
| - | chr12 | 48240466 | 48240466 | T | A | exonic | VDR | nonsynonymous | LUAD|1|543|0.00184 |
| - | chr12 | 48251014 | 48251014 | C | T | exonic | VDR | nonsynonymous | LUSC|1|178|0.00562 |
| - | chr12 | 48238712 | 48238712 | G | A | exonic | VDR | synonymous | PAAD|1|185|0.00541 |
| - | chr12 | 48251023 | 48251023 | G | A | exonic | VDR | nonsynonymous | GBMLGG|1|820|0.00122,LGG|1|530|0.00189,SKCM|1|368|0.00272,UCEC|2|248|0.00806 |
| - | chr12 | 48272780 | 48272780 | C | G | exonic | VDR | nonsynonymous | LUAD|1|543|0.00184 |
| - | chr12 | 48238574 | 48238574 | C | T | exonic | VDR | synonymous | STAD|1|395|0.00253,STES|1|395|0.00253 |
| - | chr12 | 48238710 | 48238710 | C | T | exonic | VDR | nonsynonymous | COADREAD|1|489|0.00204,READ|1|122|0.00820 |
| - | chr12 | 48251368 | 48251368 | C | T | exonic | VDR | synonymous | STAD|1|395|0.00253,STES|1|395|0.00253 |
| - | chr12 | 48251431 | 48251431 | C | T | exonic | VDR | nonsynonymous | CESC|1|194|0.00515 |
| rs121909790 | chr12 | 48272799 | 48272799 | C | T | exonic | VDR | nonsynonymous | UCEC|1|248|0.00403 |
| rs190607107 | chr12 | 48240460 | 48240460 | C | T | exonic | VDR | nonsynonymous | BLCA|1|396|0.00253 |
| rs371655308 | chr12 | 48251360 | 48251360 | C | T | exonic | VDR | nonsynonymous | UCEC|1|248|0.00403 |
| - | chr12 | 48272773 | 48272773 | C | T | exonic | VDR | nonsynonymous | SKCM|1|368|0.00272 |
| rs144628070 | chr12 | 48251338 | 48251338 | G | A | exonic | VDR | synonymous | LUAD|1|543|0.00184 |
| rs368961482 | chr12 | 48238691 | 48238691 | C | T | exonic | VDR | synonymous | COAD|1|367|0.00272,COADREAD|1|489|0.00204 |
| - | chr12 | 48238661 | 48238661 | G | A | exonic | VDR | synonymous | LUAD|1|543|0.00184 |
| - | chr12 | 48249477 | 48249477 | C | T | exonic | VDR | nonsynonymous | ACC|1|90|0.01111 |
| rs752590757 | chr12 | 48251388 | 48251388 | G | A | exonic | VDR | nonsynonymous | STAD|1|395|0.00253,STES|1|395|0.00253 |
| - | chr12 | 48240547 | 48240547 | G | A | exonic | VDR | nonsynonymous | STAD|1|395|0.00253,STES|1|395|0.00253 |
| - | chr12 | 48240513 | 48240513 | G | A | exonic | VDR | synonymous | SKCM|2|368|0.00543 |
| rs141329158 | chr12 | 48240127 | 48240127 | C | T | exonic | VDR | nonsynonymous | UCEC|1|248|0.00403 |
| - | chr12 | 48272841 | 48272841 | T | C | exonic | VDR | nonsynonymous | GBMLGG|1|820|0.00122,LGG|1|530|0.00189 |
| - | chr12 | 48272749 | 48272749 | A | G | splicing | VDR | splicing | STAD|1|395|0.00253,STES|1|395|0.00253 |
| - | chr12 | 48258886 | 48258886 | C | T | exonic | VDR | nonsynonymous | UCEC|2|248|0.00806 |
| - | chr12 | 48240510 | 48240510 | G | A | exonic | VDR | synonymous | SKCM|2|368|0.00543 |
| rs4987032 | chr12 | 48238763 | 48238763 | C | T | exonic | VDR | synonymous | LUSC|1|178|0.00562 |
| - | chr12 | 48272843 | 48272843 | C | G | exonic | VDR | synonymous | BLCA|1|396|0.00253 |
| rs757881350 | chr12 | 48240527 | 48240527 | G | A | exonic | VDR | nonsynonymous | THCA|1|504|0.00198 |
| - | chr12 | 48238559 | 48238559 | C | A | exonic | VDR | synonymous | LUAD|4|543|0.00737 |
| - | chr12 | 48258928 | 48258928 | C | T | exonic | VDR | nonsynonymous | PRAD|1|499|0.00200 |
| rs565845200 | chr12 | 48249571 | 48249571 | C | T | exonic | VDR | synonymous | LUSC|1|178|0.00562 |
| - | chr12 | 48258890 | 48258890 | G | A | exonic | VDR | stopgain | SKCM|1|368|0.00272 |
| - | chr12 | 48249476 | 48249476 | G | A | exonic | VDR | nonsynonymous | SKCM|1|368|0.00272 |
| rs746128447 | chr12 | 48240450 | 48240450 | G | A | exonic | VDR | synonymous | COAD|1|367|0.00272,COADREAD|1|489|0.00204 |
| - | chr12 | 48272866 | 48272866 | G | A | exonic | VDR | nonsynonymous | SKCM|1|368|0.00272 |
| - | chr12 | 48238609 | 48238609 | G | C | exonic | VDR | nonsynonymous | ESCA|1|185|0.00541 |
| rs140864473 | chr12 | 48251320 | 48251320 | G | A | exonic | VDR | synonymous | PRAD|1|499|0.00200 |
| - | chr12 | 48251018 | 48251018 | C | G | exonic | VDR | synonymous | LUSC|1|178|0.00562 |
| - | chr12 | 48240573 | 48240573 | G | T | exonic | VDR | nonsynonymous | COAD|1|367|0.00272,COADREAD|1|489|0.00204,ESCA|1|185|0.00541 |
| - | chr12 | 48238555 | 48238555 | C | T | exonic | VDR | nonsynonymous | UCEC|1|248|0.00403 |
| - | chr12 | 48240170 | 48240170 | G | T | exonic | VDR | nonsynonymous | TGCT|1|155|0.00645 |
| rs377423996 | chr12 | 48238785 | 48238785 | C | T | exonic | VDR | nonsynonymous | COAD|1|367|0.00272,COADREAD|1|489|0.00204 |
| - | chr12 | 48238538 | 48238538 | C | A | exonic | VDR | nonsynonymous | HNSC|1|512|0.00195 |
| - | chr12 | 48272814 | 48272814 | C | G | exonic | VDR | nonsynonymous | KIPAN|1|799|0.00125,KIRC|1|451|0.00222 |
| rs147496897 | chr12 | 48272845 | 48272845 | G | A | exonic | VDR | nonsynonymous | KICH|1|66|0.01515,KIPAN|1|799|0.00125 |
| - | chr12 | 48272874 | 48272874 | G | A | exonic | VDR | nonsynonymous | GBMLGG|1|820|0.00122,LGG|1|530|0.00189,LUSC|1|178|0.00562 |
| - | chr12 | 48249545 | 48249545 | C | A | exonic | VDR | nonsynonymous | LUSC|1|178|0.00562 |
| rs749838232 | chr12 | 48238764 | 48238764 | G | A | exonic | VDR | nonsynonymous | OV|1|469|0.00213 |
| rs543098804 | chr12 | 48251311 | 48251311 | G | C | exonic | VDR | synonymous | OV|1|469|0.00213 |
| - | chr12 | 48238570 | 48238570 | T | C | exonic | VDR | nonsynonymous | HNSC|1|512|0.00195 |
| - | chr12 | 48240182 | 48240182 | C | T | exonic | VDR | synonymous | BRCA|1|982|0.00102 |
| - | chr12 | 48250914 | 48250914 | G | C | exonic | VDR | stopgain | BLCA|1|396|0.00253 |
| - | chr12 | 48238617 | 48238617 | T | A | exonic | VDR | nonsynonymous | LUSC|1|178|0.00562 |
| TF_name | Disease_name | Disease_class | Disease_semantic_type | TF_disease_source |
|---|---|---|---|---|
| VDR | Osteoporosis, Age-Related | C05;C18 | Disease or Syndrome | CTD_human |
| VDR | Alopecia | C17;C23 | Disease or Syndrome | CTD_human |
| VDR | Bipolar Disorder | F03 | Mental or Behavioral Dysfunction | PSYGENET |
| VDR | Malignant neoplasm of breast | C04;C17 | Neoplastic Process | CTD_human |
| VDR | Malignant Neoplasms | C04 | Neoplastic Process | CTD_human |
| VDR | Carcinoma, Transitional Cell | C04 | Neoplastic Process | CTD_human |
| VDR | Cerebral Infarction | C10;C14 | Disease or Syndrome | CTD_human |
| VDR | Epilepsy, Temporal Lobe | C10 | Disease or Syndrome | CTD_human |
| VDR | Uncinate Epilepsy | C10 | Disease or Syndrome | CTD_human |
| VDR | Hereditary Diseases | C16 | Disease or Syndrome | CTD_human |
| VDR | Hypertensive disease | C14 | Disease or Syndrome | CTD_human |
| VDR | Lead Poisoning | C25 | Injury or Poisoning | CTD_human |
| VDR | Chronic Lymphocytic Leukemia | C04;C15;C20 | Neoplastic Process | CTD_human |
| VDR | Multiple Sclerosis | C10;C20 | Disease or Syndrome | CTD_human |
| VDR | Neoplasms | C04 | Neoplastic Process | CTD_human |
| VDR | Osteogenesis Imperfecta | C05;C16;C17 | Congenital Abnormality; Disease or Syndrome | GENOMICS_ENGLAND |
| VDR | Osteoporosis | C05;C18 | Disease or Syndrome | CTD_human |
| VDR | Osteoporosis, Senile | C05;C18 | Disease or Syndrome | CTD_human |
| VDR | Prostatic Neoplasms | C04;C12 | Neoplastic Process | CTD_human |
| VDR | Rickets | C05;C18 | Disease or Syndrome | CTD_human |
| VDR | Schizophrenia | F03 | Mental or Behavioral Dysfunction | PSYGENET |
| VDR | Single-Gene Defects | C16 | Disease or Syndrome | CTD_human |
| VDR | Uremia | C12;C13 | Disease or Syndrome | CTD_human |
| VDR | Vitamin D Deficiency | C18 | Disease or Syndrome | CTD_human |
| VDR | Depressive Symptoms | F01 | Sign or Symptom | PSYGENET |
| VDR | Benign Neoplasm | C04 | Neoplastic Process | CTD_human |
| VDR | Pseudopelade | C17;C23 | Disease or Syndrome | CTD_human |
| VDR | Androgenetic Alopecia | C17;C23 | Disease or Syndrome | CTD_human |
| VDR | Female pattern alopecia (disorder) | C17;C23 | Disease or Syndrome | CTD_human |
| VDR | Vitamin D-Dependent Rickets, Type 2A | C05;C12;C13;C16;C18 | Disease or Syndrome | CTD_human;UNIPROT |
| VDR | Malignant neoplasm of prostate | C04;C12 | Neoplastic Process | CTD_human |
| VDR | Epilepsy, Benign Psychomotor, Childhood | C10 | Disease or Syndrome | CTD_human |
| VDR | Epilepsy, Lateral Temporal | C10 | Disease or Syndrome | CTD_human |
| VDR | Breast Carcinoma | C04;C17 | Neoplastic Process | CTD_human |
| VDR | Cerebral Infarction, Left Hemisphere | C10;C14 | Disease or Syndrome | CTD_human |
| VDR | Cerebral Infarction, Right Hemisphere | C10;C14 | Disease or Syndrome | CTD_human |
| VDR | Anterior Choroidal Artery Infarction | C10;C14 | Disease or Syndrome | CTD_human |
| VDR | Subcortical Infarction | C10;C14 | Disease or Syndrome | CTD_human |
| VDR | Multiple Sclerosis, Acute Fulminating | C10;C20 | Disease or Syndrome | CTD_human |
| VDR | Post-Traumatic Osteoporosis | C05;C18 | Disease or Syndrome | CTD_human |
| VDR | Posterior Choroidal Artery Infarction | C10;C14 | Disease or Syndrome | CTD_human |
| VDR | Genetic Diseases, Inborn | C16 | Disease or Syndrome | CTD_human |
| VDR | Mammary Neoplasms, Human | C04;C17 | Neoplastic Process | CTD_human |
| VDR | Mammary Neoplasms | C04;C17 | Neoplastic Process | CTD_human |
| VDR | Familial Hypophosphatemic Rickets | C05;C12;C13;C16;C18 | Disease or Syndrome | ORPHANET;UNIPROT |
| VDR | Intellectual Disability | C10;C23;F01;F03 | Mental or Behavioral Dysfunction | GENOMICS_ENGLAND |
| VDR | Alopecia, Male Pattern | C17;C23 | Disease or Syndrome | CTD_human |
| pathway_ID | pathway_name | pathway_source | gene_number | edge_number |
|---|---|---|---|---|
| pathway0001883 | Retinoic acid receptors-mediated signaling | pid | 30 | 235 |
| pathway0001947 | RXR and RAR heterodimerization with other nuclear receptor | pid | 26 | 164 |
| pathway0002393 | Validated transcriptional targets of deltaNp63 isoforms | pid | 47 | 101 |
| pathway0002431 | Vitamin D metabolism and pathway | panther | 6 | 6 |
| pathway0002685 | Hs_Drug_Induction_of_Bile_Acid_Pathway_WP2289_88593 | wikipathways | 9 | 12 |
| GO_term_name | GO_term_type | TF_name |
|---|---|---|
| GO_POSITIVE_REGULATION_OF_EPITHELIAL_CELL_DIFFERENTIATION | BP | VDR |
| GO_DIGESTION | BP | VDR |
| GO_MAMMARY_GLAND_MORPHOGENESIS | BP | VDR |
| GO_POSITIVE_REGULATION_OF_KERATINOCYTE_DIFFERENTIATION | BP | VDR |
| GO_CELLULAR_RESPONSE_TO_LIPID | BP | VDR |
| GO_MAMMARY_GLAND_EPITHELIUM_DEVELOPMENT | BP | VDR |
| GO_POSITIVE_REGULATION_OF_EPIDERMAL_CELL_DIFFERENTIATION | BP | VDR |
| GO_REGULATION_OF_OXIDOREDUCTASE_ACTIVITY | BP | VDR |
| GO_REGULATION_OF_VITAMIN_METABOLIC_PROCESS | BP | VDR |
| GO_DECIDUALIZATION | BP | VDR |
| GO_REGULATION_OF_LIPID_METABOLIC_PROCESS | BP | VDR |
| GO_REGULATION_OF_KERATINOCYTE_PROLIFERATION | BP | VDR |
| GO_POSITIVE_REGULATION_OF_EPIDERMIS_DEVELOPMENT | BP | VDR |
| GO_MAMMARY_GLAND_DEVELOPMENT | BP | VDR |
| GO_POSITIVE_REGULATION_OF_TISSUE_REMODELING | BP | VDR |
| GO_TRANSCRIPTION_INITIATION_FROM_RNA_POLYMERASE_II_PROMOTER | BP | VDR |
| GO_DIGESTIVE_SYSTEM_PROCESS | BP | VDR |
| GO_CELLULAR_RESPONSE_TO_NUTRIENT | BP | VDR |
| GO_REGULATION_OF_EPIDERMAL_CELL_DIFFERENTIATION | BP | VDR |
| GO_RESPONSE_TO_VITAMIN_D | BP | VDR |
| GO_POSITIVE_REGULATION_OF_OXIDOREDUCTASE_ACTIVITY | BP | VDR |
| GO_MATERNAL_PROCESS_INVOLVED_IN_FEMALE_PREGNANCY | BP | VDR |
| GO_INTRACELLULAR_RECEPTOR_SIGNALING_PATHWAY | BP | VDR |
| GO_RESPONSE_TO_VITAMIN | BP | VDR |
| GO_REGULATION_OF_KERATINOCYTE_DIFFERENTIATION | BP | VDR |
| GO_REGULATION_OF_STEROID_BIOSYNTHETIC_PROCESS | BP | VDR |
| GO_REGULATION_OF_STEROID_METABOLIC_PROCESS | BP | VDR |
| GO_TUBE_MORPHOGENESIS | BP | VDR |
| GO_CELLULAR_RESPONSE_TO_VITAMIN | BP | VDR |
| GO_CELLULAR_RESPONSE_TO_VITAMIN_D | BP | VDR |
| GO_REGULATION_OF_ALCOHOL_BIOSYNTHETIC_PROCESS | BP | VDR |
| GO_MATERNAL_PLACENTA_DEVELOPMENT | BP | VDR |
| GO_RESPONSE_TO_ALCOHOL | BP | VDR |
| GO_MAMMARY_GLAND_DUCT_MORPHOGENESIS | BP | VDR |
| GO_BRANCHING_INVOLVED_IN_MAMMARY_GLAND_DUCT_MORPHOGENESIS | BP | VDR |
| GO_INTESTINAL_ABSORPTION | BP | VDR |
| GO_NEGATIVE_REGULATION_OF_KERATINOCYTE_PROLIFERATION | BP | VDR |
| GO_LACTATION | BP | VDR |
| GO_RNA_POLYMERASE_II_TRANSCRIPTION_FACTOR_COMPLEX | CC | VDR |
| GO_TRANSCRIPTION_FACTOR_ACTIVITY_DIRECT_LIGAND_REGULATED_SEQUENCE_SPECIFIC_DNA_BINDING | MF | VDR |
| GO_ALCOHOL_BINDING | MF | VDR |
| GO_RETINOIC_ACID_RECEPTOR_BINDING | MF | VDR |
| GO_TRANSCRIPTION_FACTOR_BINDING | MF | VDR |
| GO_RETINOID_X_RECEPTOR_BINDING | MF | VDR |