Gene Page: SMAD9

Summary ?
GeneID4093
SymbolSMAD9
SynonymsMADH6|MADH9|PPH2|SMAD8|SMAD8/9|SMAD8A|SMAD8B
DescriptionSMAD family member 9
ReferenceMIM:603295|HGNC:HGNC:6774|Ensembl:ENSG00000120693|Vega:OTTHUMG00000016740
Gene typeprotein-coding
Map location13q12-q14
Pascal p-value0.804
Sherlock p-value0.007
eGeneCaudate basal ganglia
Cerebellum
Cortex
Nucleus accumbens basal ganglia
Putamen basal ganglia

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 2 
NetworkShortest path distance of core genes in the Human protein-protein interaction networkContribution to shortest path in PPI network: 0.0124 

Section I. Genetics and epigenetics annotation

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs93154501337408734SMAD9ENSG00000120693.91.644E-6086168gtex_brain_putamen_basal
rs93154511337410696SMAD9ENSG00000120693.91.644E-6084206gtex_brain_putamen_basal
rs49434231337412644SMAD9ENSG00000120693.92.333E-6082258gtex_brain_putamen_basal
rs96350721337416234SMAD9ENSG00000120693.92.929E-6078668gtex_brain_putamen_basal
rs73251871337417048SMAD9ENSG00000120693.91.643E-6077854gtex_brain_putamen_basal
rs6094181337417427SMAD9ENSG00000120693.91.643E-6077475gtex_brain_putamen_basal
rs3977308581337418491SMAD9ENSG00000120693.91.643E-6076411gtex_brain_putamen_basal
rs602709731337419042SMAD9ENSG00000120693.93.665E-6075860gtex_brain_putamen_basal
rs6428661337420348SMAD9ENSG00000120693.91.643E-6074554gtex_brain_putamen_basal
rs49434311337423032SMAD9ENSG00000120693.92.929E-6071870gtex_brain_putamen_basal
rs4959721337445398SMAD9ENSG00000120693.93.767E-6049504gtex_brain_putamen_basal
rs95761261337446711SMAD9ENSG00000120693.93.298E-6048191gtex_brain_putamen_basal
rs95761271337448551SMAD9ENSG00000120693.93.004E-6046351gtex_brain_putamen_basal
rs3775748201337451640SMAD9ENSG00000120693.92.038E-6043262gtex_brain_putamen_basal
rs95761291337455391SMAD9ENSG00000120693.92.005E-6039511gtex_brain_putamen_basal
rs95661681337457290SMAD9ENSG00000120693.92.005E-6037612gtex_brain_putamen_basal
rs95761301337457686SMAD9ENSG00000120693.92.001E-6037216gtex_brain_putamen_basal
rs95761311337467578SMAD9ENSG00000120693.91.67E-6027324gtex_brain_putamen_basal
rs95761321337480201SMAD9ENSG00000120693.92.821E-7014701gtex_brain_putamen_basal
rs95761341337481694SMAD9ENSG00000120693.91.088E-6013208gtex_brain_putamen_basal
rs124277321337489555SMAD9ENSG00000120693.92.142E-605347gtex_brain_putamen_basal
rs3704521851337491724SMAD9ENSG00000120693.97.235E-703178gtex_brain_putamen_basal
rs95661691337492472SMAD9ENSG00000120693.91.005E-602430gtex_brain_putamen_basal

Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

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
GenePearson's Correlation Spearman's Correlation
DBNDD20.970.94
PLLP0.960.95
NINJ20.960.93
CMTM50.930.95
ELOVL10.930.92
TSPAN150.930.90
MOG0.920.95
GJB10.920.94
RNASE10.920.93
RTKN0.920.93
Top 10 negatively co-expressed genes
GenePearson'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 functionGO termEvidenceNeuro keywordsPubMed ID
GO:0003700transcription factor activityIEA-
GO:0005515protein bindingIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0030902hindbrain developmentIEABrain (GO term level: 8)-
GO:0030901midbrain developmentIEABrain (GO term level: 8)-
GO:0006355regulation of transcription, DNA-dependentIEA-
GO:0006350transcriptionIEA-
GO:0007179transforming growth factor beta receptor signaling pathwayIEA-
GO:0030509BMP signaling pathwayEXP15621726 
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005829cytosolEXP9436979 |17356069 
GO:0005622intracellularTAS9256479 
GO:0005634nucleusIEA-
GO:0005654nucleoplasmEXP11121043 
GO:0005667transcription factor complexIEA-
GO:0005737cytoplasmIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG TGF BETA SIGNALING PATHWAY 8664All SZGR 2.0 genes in this pathway
PID BMP PATHWAY 4231All SZGR 2.0 genes in this pathway
PID ALK1 PATHWAY 2621All SZGR 2.0 genes in this pathway
PID ALK2 PATHWAY 119All SZGR 2.0 genes in this pathway
CHARAFE BREAST CANCER LUMINAL VS MESENCHYMAL DN 460312All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED DN 805505All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA ANAPLASTIC DN 537339All SZGR 2.0 genes in this pathway
BEGUM TARGETS OF PAX3 FOXO1 FUSION DN 4534All SZGR 2.0 genes in this pathway
PEREZ TP53 TARGETS 1174695All SZGR 2.0 genes in this pathway
PEREZ TP63 TARGETS 355243All SZGR 2.0 genes in this pathway
PEREZ TP53 AND TP63 TARGETS 205145All SZGR 2.0 genes in this pathway
SCHLOSSER SERUM RESPONSE UP 13493All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS STEM CELL AND PROGENITOR 681420All SZGR 2.0 genes in this pathway
LOPES METHYLATED IN COLON CANCER DN 2826All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER WITH H3K27ME3 UP 295149All SZGR 2.0 genes in this pathway
ACEVEDO METHYLATED IN LIVER CANCER DN 940425All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2 491319All SZGR 2.0 genes in this pathway