Gene Page: SMAD1
Summary ?
GeneID | 4086 |
Symbol | SMAD1 |
Synonyms | BSP-1|BSP1|JV4-1|JV41|MADH1|MADR1 |
Description | SMAD family member 1 |
Reference | MIM:601595|HGNC:HGNC:6767|HPRD:03356| |
Gene type | protein-coding |
Map location | 4q31 |
Pascal p-value | 0.039 |
Sherlock p-value | 0.902 |
eGene | Myers' cis & trans Meta |
Gene in Data Sources
Gene set name | Method of gene set | Description | Info |
---|---|---|---|
CV:PGCnp | Genome-wide Association Study | GWAS | |
GO_Annotation | Mapping neuro-related keywords to Gene Ontology annotations | Hits with neuro-related keywords: 2 |
Section I. Genetics and epigenetics annotation
eQTL annotation
SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
---|---|---|---|---|---|---|---|---|
rs11100879 | chr4 | 146360411 | SMAD1 | 4086 | 0.01 | cis | ||
rs11100883 | chr4 | 146450969 | SMAD1 | 4086 | 1.967E-4 | cis | ||
rs2036138 | chr4 | 146484861 | SMAD1 | 4086 | 2.383E-9 | cis | ||
rs11100883 | chr4 | 146450969 | SMAD1 | 4086 | 0.02 | trans | ||
rs2036138 | chr4 | 146484861 | SMAD1 | 4086 | 5.76E-7 | trans |
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 |
SLC25A18 | 0.50 | 0.59 |
P2RY14 | 0.50 | 0.56 |
AC011427.1 | 0.50 | 0.57 |
GLUL | 0.49 | 0.58 |
NDRG2 | 0.48 | 0.58 |
ALDOC | 0.48 | 0.56 |
ADHFE1 | 0.48 | 0.54 |
GPER | 0.48 | 0.58 |
SNTA1 | 0.48 | 0.57 |
CLDN10 | 0.48 | 0.58 |
Top 10 negatively co-expressed genes | ||
Gene | Pearson's Correlation | Spearman's Correlation |
SAAL1 | -0.46 | -0.57 |
CNOT10 | -0.46 | -0.54 |
TRA2A | -0.46 | -0.51 |
PGBD1 | -0.46 | -0.51 |
USPL1 | -0.46 | -0.54 |
ZNF589 | -0.46 | -0.50 |
RAE1 | -0.46 | -0.51 |
ZNF329 | -0.46 | -0.49 |
ZNF182 | -0.46 | -0.50 |
ZNF509 | -0.45 | -0.50 |
Section III. Gene Ontology annotation
Molecular function | GO term | Evidence | Neuro keywords | PubMed ID |
---|---|---|---|---|
GO:0005057 | receptor signaling protein activity | NAS | 8653785 |10708949 | |
GO:0003700 | transcription factor activity | IEA | - | |
GO:0003702 | RNA polymerase II transcription factor activity | IEA | - | |
GO:0005515 | protein binding | IPI | 15781469 | |
GO:0016563 | transcription activator activity | NAS | - | |
Biological process | GO term | 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:0000165 | MAPKKK cascade | IEA | - | |
GO:0006355 | regulation of transcription, DNA-dependent | IEA | - | |
GO:0006350 | transcription | IEA | - | |
GO:0007165 | signal transduction | NAS | 9759503 | |
GO:0007179 | transforming growth factor beta receptor signaling pathway | NAS | 8663601 | |
GO:0008285 | negative regulation of cell proliferation | IEA | - | |
GO:0009880 | embryonic pattern specification | ISS | - | |
GO:0007276 | gamete generation | IEA | - | |
GO:0042592 | homeostatic process | IEA | - | |
GO:0030509 | BMP signaling pathway | EXP | 15621726 | |
GO:0030509 | BMP signaling pathway | ISS | - | |
GO:0045944 | positive regulation of transcription from RNA polymerase II promoter | IEA | - | |
Cellular component | GO term | Evidence | Neuro keywords | PubMed ID |
GO:0005829 | cytosol | EXP | 9436979 |17356069 | |
GO:0005622 | intracellular | IEA | - | |
GO:0005622 | intracellular | NAS | 10647776 | |
GO:0005634 | nucleus | NAS | 9759503 | |
GO:0005654 | nucleoplasm | EXP | 11121043 | |
GO:0005667 | transcription factor complex | IEA | - | |
GO:0005737 | cytoplasm | IEA | - | |
GO:0016021 | integral to membrane | NAS | 8663601 |
Section IV. Protein-protein interaction annotation
Interactors | Aliases B | Official full name B | Experimental | Source | PubMed ID |
---|---|---|---|---|---|
ACVR1 | ACTRI | ACVR1A | ACVRLK2 | ALK2 | FOP | SKR1 | TSRI | activin A receptor, type I | - | HPRD | 9748228 |10583507 |10652350 |
ACVR1 | ACTRI | ACVR1A | ACVRLK2 | ALK2 | FOP | SKR1 | TSRI | activin A receptor, type I | Affinity Capture-Western | BioGRID | 9748228 |10652350 |
BMP7 | OP-1 | bone morphogenetic protein 7 | Phenotypic Suppression | BioGRID | 11438941 |
BMPR1A | 10q23del | ACVRLK3 | ALK3 | CD292 | bone morphogenetic protein receptor, type IA | - | HPRD | 11438941 |
CREBBP | CBP | KAT3A | RSTS | CREB binding protein | Affinity Capture-Western | BioGRID | 10673036 |11239394 |
DVL1 | DVL | MGC54245 | dishevelled, dsh homolog 1 (Drosophila) | Reconstituted Complex | BioGRID | 12650946 |
ECSIT | SITPEC | ECSIT homolog (Drosophila) | - | HPRD | 14633973 |
EP300 | KAT3B | p300 | E1A binding protein p300 | - | HPRD,BioGRID | 10673036 |
ERBB2IP | ERBIN | LAP2 | erbb2 interacting protein | - | HPRD,BioGRID | 12650946 |
FOXG1 | BF1 | BF2 | FHKL3 | FKH2 | FKHL1 | FKHL2 | FKHL3 | FKHL4 | FOXG1A | FOXG1B | FOXG1C | HBF-1 | HBF-2 | HBF-3 | HBF-G2 | HBF2 | HFK1 | HFK2 | HFK3 | KHL2 | QIN | forkhead box G1 | - | HPRD,BioGRID | 11387330 |
GDF6 | BMP13 | CDMP2 | KFS | KFSL | MGC158100 | MGC158101 | SGM1 | growth differentiation factor 6 | - | HPRD | 15246821 |
GLI3 | ACLS | GCPS | PAP-A | PAPA | PAPA1 | PAPB | PHS | PPDIV | GLI-Kruppel family member GLI3 | - | HPRD | 9843199 |
HIPK2 | DKFZp686K02111 | FLJ23711 | PRO0593 | homeodomain interacting protein kinase 2 | - | HPRD,BioGRID | 12874272 |
HOXC8 | HOX3 | HOX3A | homeobox C8 | - | HPRD,BioGRID | 10224145 |11139569 |
LEF1 | DKFZp586H0919 | TCF1ALPHA | lymphoid enhancer-binding factor 1 | - | HPRD,BioGRID | 10890911 |
LEMD3 | MAN1 | LEM domain containing 3 | LEMD3 interacts with Smad1. This interaction was modelled on a demonstrated interaction between human LEMD3 and mouse Smad1. | BIND | 15489854 |
NEDD9 | CAS-L | CAS2 | CASL | CASS2 | HEF1 | dJ49G10.2 | dJ761I2.1 | neural precursor cell expressed, developmentally down-regulated 9 | - | HPRD,BioGRID | 11118211 |
NEUROG1 | AKA | Math4C | NEUROD3 | bHLHa6 | ngn1 | neurogenin 1 | - | HPRD,BioGRID | 11239394 |
OAZ3 | AZ3 | OAZ-t | TISP15 | ornithine decarboxylase antizyme 3 | Two-hybrid | BioGRID | 11438941 |
PARD3B | ALS2CR19 | MGC16131 | PAR3B | PAR3L | PAR3LC | PAR3beta | Par3Lb | par-3 partitioning defective 3 homolog B (C. elegans) | Reconstituted Complex | BioGRID | 12650946 |
PSMB4 | HN3 | HsN3 | PROS26 | proteasome (prosome, macropain) subunit, beta type, 4 | - | HPRD,BioGRID | 12097147 |
RAN | ARA24 | Gsp1 | TC4 | RAN, member RAS oncogene family | SMAD1 interacts with RAN. This interaction was modeled on a demonstrated interaction between human SMAD1 and mouse RAN. | BIND | 15761153 |
RPS27A | CEP80 | HUBCEP80 | UBA80 | UBCEP1 | UBCEP80 | ribosomal protein S27a | Two-hybrid | BioGRID | 11438941 |
RUNX1 | AML1 | AML1-EVI-1 | AMLCR1 | CBFA2 | EVI-1 | PEBP2aB | runt-related transcription factor 1 | Affinity Capture-Western | BioGRID | 10531362 |
RUNX2 | AML3 | CBFA1 | CCD | CCD1 | MGC120022 | MGC120023 | OSF2 | PEA2aA | PEBP2A1 | PEBP2A2 | PEBP2aA | PEBP2aA1 | runt-related transcription factor 2 | Affinity Capture-Western | BioGRID | 10531362 |10962029 |
RUNX3 | AML2 | CBFA3 | FLJ34510 | MGC16070 | PEBP2aC | runt-related transcription factor 3 | Affinity Capture-Western | BioGRID | 10531362 |
SKI | SKV | v-ski sarcoma viral oncogene homolog (avian) | Affinity Capture-Western Reconstituted Complex | BioGRID | 12874272 |
SKIL | SNO | SnoA | SnoN | SKI-like oncogene | Smad1 interacts with SnoN. This interaction was modeled on a demonstrated interaction between SnoN from an unspecified source and human Smad1. | BIND | 12426322 |
SMAD4 | DPC4 | JIP | MADH4 | SMAD family member 4 | - | HPRD | 10400705 |11700304 |
SMAD4 | DPC4 | JIP | MADH4 | SMAD family member 4 | Affinity Capture-Western Co-fractionation | BioGRID | 10531362 |11700304 |12874272 |
SMAD4 | DPC4 | JIP | MADH4 | SMAD family member 4 | Smad4 interacts with Smad1. | BIND | 15761153 |
SMAD6 | HsT17432 | MADH6 | MADH7 | SMAD family member 6 | - | HPRD | 11483516 |
SMURF2 | DKFZp686F0270 | MGC138150 | SMAD specific E3 ubiquitin protein ligase 2 | SMAD1 interacts with SMURF2. | BIND | 15761153 |
SMURF2 | DKFZp686F0270 | MGC138150 | SMAD specific E3 ubiquitin protein ligase 2 | - | HPRD,BioGRID | 11016919 |
SNIP1 | FLJ12553 | RP3-423B22.3 | dJ423B22.2 | Smad nuclear interacting protein 1 | - | HPRD,BioGRID | 10887155 |
SNX6 | MGC3157 | MSTP010 | TFAF2 | sorting nexin 6 | - | HPRD | 11279102 |
STAT3 | APRF | FLJ20882 | HIES | MGC16063 | signal transducer and activator of transcription 3 (acute-phase response factor) | Affinity Capture-Western | BioGRID | 10205054 |
STUB1 | CHIP | HSPABP2 | NY-CO-7 | SDCCAG7 | UBOX1 | STIP1 homology and U-box containing protein 1 | Smad1 interacts with CHIP. This interaction was modeled on a demonstrated interaction between Smad1 and CHIP, both from an unspecified species. | BIND | 15708501 |
TGIF1 | HPE4 | MGC39747 | MGC5066 | TGIF | TGFB-induced factor homeobox 1 | Affinity Capture-Western | BioGRID | 10199400 |
TOB1 | APRO6 | MGC104792 | MGC34446 | PIG49 | TOB | TROB | TROB1 | transducer of ERBB2, 1 | - | HPRD,BioGRID | 11163184 |
UBA52 | CEP52 | HUBCEP52 | MGC126879 | MGC126881 | MGC57125 | RPL40 | ubiquitin A-52 residue ribosomal protein fusion product 1 | Two-hybrid | BioGRID | 11438941 |
XPO1 | CRM1 | DKFZp686B1823 | exportin 1 (CRM1 homolog, yeast) | - | HPRD | 12519765 |
ZEB1 | AREB6 | BZP | DELTA-EF1 | MGC133261 | NIL-2-A | NIL-2A | NIL2A | TCF8 | ZEB | ZFHEP | ZFHX1A | zinc finger E-box binding homeobox 1 | Affinity Capture-Western | BioGRID | 12743038 |
ZEB2 | KIAA0569 | SIP-1 | SIP1 | SMADIP1 | ZFHX1B | zinc finger E-box binding homeobox 2 | - | HPRD | 10400677 |
ZNF423 | Ebfaz | KIAA0760 | MGC138520 | MGC138522 | OAZ | Roaz | ZFP423 | Zfp104 | zinc finger protein 423 | - | HPRD,BioGRID | 10660046 |
ZNF521 | DKFZp564D0764 | EHZF | Evi3 | MGC142182 | MGC142208 | zinc finger protein 521 | - | HPRD | 14630787 |
ZNF8 | HF.18 | Zfp128 | zinc finger protein 8 | - | HPRD | 12370310 |
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 |
BIOCARTA ALK PATHWAY | 37 | 29 | All SZGR 2.0 genes in this pathway |
BIOCARTA CTCF PATHWAY | 23 | 18 | All SZGR 2.0 genes in this pathway |
PID ERBB1 DOWNSTREAM PATHWAY | 105 | 78 | 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 |
REACTOME SIGNALING BY BMP | 23 | 15 | All SZGR 2.0 genes in this pathway |
DAVICIONI TARGETS OF PAX FOXO1 FUSIONS UP | 255 | 177 | All SZGR 2.0 genes in this pathway |
ZHOU INFLAMMATORY RESPONSE FIMA DN | 284 | 156 | All SZGR 2.0 genes in this pathway |
JAATINEN HEMATOPOIETIC STEM CELL UP | 316 | 190 | All SZGR 2.0 genes in this pathway |
RODRIGUES THYROID CARCINOMA ANAPLASTIC DN | 537 | 339 | All SZGR 2.0 genes in this pathway |
KOKKINAKIS METHIONINE DEPRIVATION 48HR UP | 128 | 95 | All SZGR 2.0 genes in this pathway |
KOKKINAKIS METHIONINE DEPRIVATION 96HR UP | 117 | 84 | All SZGR 2.0 genes in this pathway |
RIZ ERYTHROID DIFFERENTIATION 12HR | 43 | 35 | All SZGR 2.0 genes in this pathway |
TURJANSKI MAPK1 AND MAPK2 TARGETS | 12 | 10 | All SZGR 2.0 genes in this pathway |
HUMMERICH SKIN CANCER PROGRESSION UP | 88 | 58 | All SZGR 2.0 genes in this pathway |
SCHLOSSER SERUM RESPONSE DN | 712 | 443 | All SZGR 2.0 genes in this pathway |
NUYTTEN EZH2 TARGETS UP | 1037 | 673 | All SZGR 2.0 genes in this pathway |
GOTZMANN EPITHELIAL TO MESENCHYMAL TRANSITION UP | 69 | 55 | All SZGR 2.0 genes in this pathway |
MORI PLASMA CELL DN | 33 | 20 | All SZGR 2.0 genes in this pathway |
SMITH TERT TARGETS UP | 145 | 91 | All SZGR 2.0 genes in this pathway |
TARTE PLASMA CELL VS PLASMABLAST UP | 398 | 262 | All SZGR 2.0 genes in this pathway |
BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS | 882 | 572 | All SZGR 2.0 genes in this pathway |
FERRANDO T ALL WITH MLL ENL FUSION UP | 87 | 67 | All SZGR 2.0 genes in this pathway |
HADDAD B LYMPHOCYTE PROGENITOR | 293 | 193 | All SZGR 2.0 genes in this pathway |
IGLESIAS E2F TARGETS UP | 151 | 103 | All SZGR 2.0 genes in this pathway |
RAMALHO STEMNESS UP | 206 | 118 | All SZGR 2.0 genes in this pathway |
MCCLUNG DELTA FOSB TARGETS 2WK | 48 | 36 | All SZGR 2.0 genes in this pathway |
BLALOCK ALZHEIMERS DISEASE UP | 1691 | 1088 | All SZGR 2.0 genes in this pathway |
WEIGEL OXIDATIVE STRESS BY HNE AND TBH | 60 | 42 | All SZGR 2.0 genes in this pathway |
ZHANG ANTIVIRAL RESPONSE TO RIBAVIRIN DN | 51 | 32 | All SZGR 2.0 genes in this pathway |
IVANOVA HEMATOPOIESIS STEM CELL AND PROGENITOR | 681 | 420 | All SZGR 2.0 genes in this pathway |
BROWNE HCMV INFECTION 6HR DN | 160 | 101 | All SZGR 2.0 genes in this pathway |
MONNIER POSTRADIATION TUMOR ESCAPE UP | 393 | 244 | All SZGR 2.0 genes in this pathway |
MARTINEZ RB1 TARGETS UP | 673 | 430 | All SZGR 2.0 genes in this pathway |
MARTINEZ TP53 TARGETS DN | 593 | 372 | All SZGR 2.0 genes in this pathway |
MARTINEZ RB1 AND TP53 TARGETS DN | 591 | 366 | All SZGR 2.0 genes in this pathway |
IZADPANAH STEM CELL ADIPOSE VS BONE DN | 108 | 68 | All SZGR 2.0 genes in this pathway |
MATZUK EMBRYONIC GERM CELL | 19 | 16 | All SZGR 2.0 genes in this pathway |
BOQUEST STEM CELL DN | 216 | 143 | All SZGR 2.0 genes in this pathway |
BOYLAN MULTIPLE MYELOMA C D DN | 252 | 155 | All SZGR 2.0 genes in this pathway |
GU PDEF TARGETS UP | 71 | 49 | All SZGR 2.0 genes in this pathway |
YOSHIMURA MAPK8 TARGETS DN | 366 | 257 | All SZGR 2.0 genes in this pathway |
HOSHIDA LIVER CANCER LATE RECURRENCE DN | 69 | 48 | All SZGR 2.0 genes in this pathway |
YAGI AML WITH 11Q23 REARRANGED | 351 | 238 | All SZGR 2.0 genes in this pathway |
BOYLAN MULTIPLE MYELOMA PCA3 UP | 80 | 54 | All SZGR 2.0 genes in this pathway |
ZHAN MULTIPLE MYELOMA LB DN | 44 | 23 | All SZGR 2.0 genes in this pathway |
WONG ADULT TISSUE STEM MODULE | 721 | 492 | All SZGR 2.0 genes in this pathway |
KANG AR TARGETS DN | 19 | 12 | All SZGR 2.0 genes in this pathway |
LEE BMP2 TARGETS UP | 745 | 475 | All SZGR 2.0 genes in this pathway |
KOINUMA TARGETS OF SMAD2 OR SMAD3 | 824 | 528 | All SZGR 2.0 genes in this pathway |
PEDRIOLI MIR31 TARGETS DN | 418 | 245 | All SZGR 2.0 genes in this pathway |
PHONG TNF RESPONSE NOT VIA P38 | 337 | 236 | All SZGR 2.0 genes in this pathway |
Section VI. microRNA annotation
miRNA family | Target position | miRNA ID | miRNA seq | ||
---|---|---|---|---|---|
UTR start | UTR end | Match method | |||
miR-182 | 1008 | 1015 | 1A,m8 | hsa-miR-182 | UUUGGCAAUGGUAGAACUCACA |
miR-205 | 50 | 56 | 1A | hsa-miR-205 | UCCUUCAUUCCACCGGAGUCUG |
miR-26 | 46 | 53 | 1A,m8 | hsa-miR-26abrain | UUCAAGUAAUCCAGGAUAGGC |
hsa-miR-26bSZ | UUCAAGUAAUUCAGGAUAGGUU | ||||
hsa-miR-26abrain | UUCAAGUAAUCCAGGAUAGGC | ||||
hsa-miR-26bSZ | UUCAAGUAAUUCAGGAUAGGUU | ||||
miR-30-5p | 206 | 212 | 1A | hsa-miR-30a-5p | UGUAAACAUCCUCGACUGGAAG |
hsa-miR-30cbrain | UGUAAACAUCCUACACUCUCAGC | ||||
hsa-miR-30dSZ | UGUAAACAUCCCCGACUGGAAG | ||||
hsa-miR-30bSZ | UGUAAACAUCCUACACUCAGCU | ||||
hsa-miR-30e-5p | UGUAAACAUCCUUGACUGGA | ||||
hsa-miR-30a-5p | UGUAAACAUCCUCGACUGGAAG | ||||
hsa-miR-30cbrain | UGUAAACAUCCUACACUCUCAGC | ||||
hsa-miR-30dSZ | UGUAAACAUCCCCGACUGGAAG | ||||
hsa-miR-30bSZ | UGUAAACAUCCUACACUCAGCU | ||||
hsa-miR-30e-5p | UGUAAACAUCCUUGACUGGA | ||||
miR-370 | 255 | 261 | 1A | hsa-miR-370brain | GCCUGCUGGGGUGGAACCUGG |
miR-96 | 1009 | 1015 | 1A | hsa-miR-96brain | UUUGGCACUAGCACAUUUUUGC |
- SZ: miRNAs which differentially expressed in brain cortex of schizophrenia patients comparing with control samples using microarray. Click here to see the list of SZ related miRNAs.
- Brain: miRNAs which are expressed in brain based on miRNA microarray expression studies. Click here to see the list of brain related miRNAs.