Gene Page:SMAD9
Summary?
| GeneID | 4093 |
| Symbol | SMAD9 |
| Synonyms | MADH6|MADH9|PPH2|SMAD8|SMAD8/9|SMAD8A|SMAD8B |
| Description | SMAD family member 9 |
| Reference | MIM:603295|HGNC:HGNC:6774|Ensembl:ENSG00000120693|Vega:OTTHUMG00000016740 |
| Gene type | protein-coding |
| Map location | 13q12-q14 |
| Pascal p-value | 0.804 |
| Sherlock p-value | 0.007 |
| eGene | Caudate basal ganglia Cerebellum Cortex Nucleus accumbens basal ganglia Putamen basal ganglia |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| GO_Annotation | Mapping neuro-related keywords to Gene Ontology annotations | Hits with neuro-related keywords: 2 | |
| Network | Shortest path distance of core genes in the Human protein-protein interaction network | Contribution to shortest path in PPI network: 0.0124 |
Section I. Genetics and epigenetics annotation
eQTL annotation
eQTL annotation| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs9315450 | 13 | 37408734 | SMAD9 | ENSG00000120693.9 | 1.644E-6 | 0 | 86168 | gtex_brain_putamen_basal |
| rs9315451 | 13 | 37410696 | SMAD9 | ENSG00000120693.9 | 1.644E-6 | 0 | 84206 | gtex_brain_putamen_basal |
| rs4943423 | 13 | 37412644 | SMAD9 | ENSG00000120693.9 | 2.333E-6 | 0 | 82258 | gtex_brain_putamen_basal |
| rs9635072 | 13 | 37416234 | SMAD9 | ENSG00000120693.9 | 2.929E-6 | 0 | 78668 | gtex_brain_putamen_basal |
| rs7325187 | 13 | 37417048 | SMAD9 | ENSG00000120693.9 | 1.643E-6 | 0 | 77854 | gtex_brain_putamen_basal |
| rs609418 | 13 | 37417427 | SMAD9 | ENSG00000120693.9 | 1.643E-6 | 0 | 77475 | gtex_brain_putamen_basal |
| rs397730858 | 13 | 37418491 | SMAD9 | ENSG00000120693.9 | 1.643E-6 | 0 | 76411 | gtex_brain_putamen_basal |
| rs60270973 | 13 | 37419042 | SMAD9 | ENSG00000120693.9 | 3.665E-6 | 0 | 75860 | gtex_brain_putamen_basal |
| rs642866 | 13 | 37420348 | SMAD9 | ENSG00000120693.9 | 1.643E-6 | 0 | 74554 | gtex_brain_putamen_basal |
| rs4943431 | 13 | 37423032 | SMAD9 | ENSG00000120693.9 | 2.929E-6 | 0 | 71870 | gtex_brain_putamen_basal |
| rs495972 | 13 | 37445398 | SMAD9 | ENSG00000120693.9 | 3.767E-6 | 0 | 49504 | gtex_brain_putamen_basal |
| rs9576126 | 13 | 37446711 | SMAD9 | ENSG00000120693.9 | 3.298E-6 | 0 | 48191 | gtex_brain_putamen_basal |
| rs9576127 | 13 | 37448551 | SMAD9 | ENSG00000120693.9 | 3.004E-6 | 0 | 46351 | gtex_brain_putamen_basal |
| rs377574820 | 13 | 37451640 | SMAD9 | ENSG00000120693.9 | 2.038E-6 | 0 | 43262 | gtex_brain_putamen_basal |
| rs9576129 | 13 | 37455391 | SMAD9 | ENSG00000120693.9 | 2.005E-6 | 0 | 39511 | gtex_brain_putamen_basal |
| rs9566168 | 13 | 37457290 | SMAD9 | ENSG00000120693.9 | 2.005E-6 | 0 | 37612 | gtex_brain_putamen_basal |
| rs9576130 | 13 | 37457686 | SMAD9 | ENSG00000120693.9 | 2.001E-6 | 0 | 37216 | gtex_brain_putamen_basal |
| rs9576131 | 13 | 37467578 | SMAD9 | ENSG00000120693.9 | 1.67E-6 | 0 | 27324 | gtex_brain_putamen_basal |
| rs9576132 | 13 | 37480201 | SMAD9 | ENSG00000120693.9 | 2.821E-7 | 0 | 14701 | gtex_brain_putamen_basal |
| rs9576134 | 13 | 37481694 | SMAD9 | ENSG00000120693.9 | 1.088E-6 | 0 | 13208 | gtex_brain_putamen_basal |
| rs12427732 | 13 | 37489555 | SMAD9 | ENSG00000120693.9 | 2.142E-6 | 0 | 5347 | gtex_brain_putamen_basal |
| rs370452185 | 13 | 37491724 | SMAD9 | ENSG00000120693.9 | 7.235E-7 | 0 | 3178 | gtex_brain_putamen_basal |
| rs9566169 | 13 | 37492472 | SMAD9 | ENSG00000120693.9 | 1.005E-6 | 0 | 2430 | gtex_brain_putamen_basal |
Section II. Transcriptome annotation
General gene expression (GTEx)
Gene expression of temporal and spatial changes (BrainSpan)
Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.
Top co-expressed genes in brain regions
| Top 10 positively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| DBNDD2 | 0.97 | 0.94 |
| PLLP | 0.96 | 0.95 |
| NINJ2 | 0.96 | 0.93 |
| CMTM5 | 0.93 | 0.95 |
| ELOVL1 | 0.93 | 0.92 |
| TSPAN15 | 0.93 | 0.90 |
| MOG | 0.92 | 0.95 |
| GJB1 | 0.92 | 0.94 |
| RNASE1 | 0.92 | 0.93 |
| RTKN | 0.92 | 0.93 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| NKIRAS2 | -0.62 | -0.74 |
| CRMP1 | -0.59 | -0.73 |
| TUBB2B | -0.59 | -0.79 |
| KIAA1949 | -0.59 | -0.75 |
| HN1 | -0.58 | -0.72 |
| HMGB3 | -0.58 | -0.77 |
| PCDHB18 | -0.58 | -0.73 |
| YBX1 | -0.58 | -0.78 |
| TUBB | -0.58 | -0.73 |
| DPYSL3 | -0.57 | -0.72 |
Section III. Gene Ontology annotation
| Molecular function | 去的术语 | Evidence | Neuro keywords | PubMed ID |
|---|---|---|---|---|
| GO:0003700 | transcription factor activity | IEA | - | |
| GO:0005515 | protein binding | IEA | - | |
| Biological process | 去的术语 | Evidence | Neuro keywords | PubMed ID |
| GO:0030902 | hindbrain development | IEA | Brain (GO term level: 8) | - |
| GO:0030901 | midbrain development | IEA | Brain (GO term level: 8) | - |
| GO:0006355 | regulation of transcription, DNA-dependent | IEA | - | |
| GO:0006350 | transcription | IEA | - | |
| GO:0007179 | transforming growth factor beta receptor signaling pathway | IEA | - | |
| GO:0030509 | BMP signaling pathway | EXP | 15621726 | |
| Cellular component | 去的术语 | Evidence | Neuro keywords | PubMed ID |
| GO:0005829 | cytosol | EXP | 9436979|17356069 | |
| GO:0005622 | intracellular | TAS | 9256479 | |
| GO:0005634 | nucleus | IEA | - | |
| GO:0005654 | nucleoplasm | EXP | 11121043 | |
| GO:0005667 | transcription factor complex | IEA | - | |
| GO:0005737 | cytoplasm | IEA | - |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| KEGG TGF BETA SIGNALING PATHWAY | 86 | 64 | All SZGR 2.0 genes in this pathway |
| PID BMP PATHWAY | 42 | 31 | All SZGR 2.0 genes in this pathway |
| PID ALK1 PATHWAY | 26 | 21 | All SZGR 2.0 genes in this pathway |
| PID ALK2 PATHWAY | 11 | 9 | All SZGR 2.0 genes in this pathway |
| CHARAFE BREAST CANCER LUMINAL VS MESENCHYMAL DN | 460 | 312 | All SZGR 2.0 genes in this pathway |
| RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED DN | 805 | 505 | All SZGR 2.0 genes in this pathway |
| RODRIGUES THYROID CARCINOMA ANAPLASTIC DN | 537 | 339 | All SZGR 2.0 genes in this pathway |
| BEGUM P的目标AX3 FOXO1 FUSION DN | 45 | 34 | All SZGR 2.0 genes in this pathway |
| PEREZ TP53 TARGETS | 1174 | 695 | All SZGR 2.0 genes in this pathway |
| PEREZ TP63 TARGETS | 355 | 243 | All SZGR 2.0 genes in this pathway |
| PEREZ TP53 AND TP63 TARGETS | 205 | 145 | All SZGR 2.0 genes in this pathway |
| SCHLOSSER SERUM RESPONSE UP | 134 | 93 | All SZGR 2.0 genes in this pathway |
| IVANOVA HEMATOPOIESIS STEM CELL AND PROGENITOR | 681 | 420 | All SZGR 2.0 genes in this pathway |
| LOPES METHYLATED IN COLON CANCER DN | 28 | 26 | All SZGR 2.0 genes in this pathway |
| ACEVEDO LIVER CANCER WITH H3K27ME3 UP | 295 | 149 | All SZGR 2.0 genes in this pathway |
| ACEVEDO METHYLATED IN LIVER CANCER DN | 940 | 425 | All SZGR 2.0 genes in this pathway |
| MEISSNER NPC HCP WITH H3K4ME2 | 491 | 319 | All SZGR 2.0 genes in this pathway |