Gene Page:RET

Summary?
GeneID 5979
Symbol RET
Synonyms CDHF12|CDHR16|HSCR1|MEN2A|MEN2B|MTC1|PTC|RET-ELE1|RET51
Description ret proto-oncogene
Reference MIM:164761|HGNC:HGNC:9967|Ensembl:ENSG00000165731|HPRD:01266|Vega:OTTHUMG00000018024
Gene type protein-coding
Map location 10q11.2
Pascal p-value 0.807
DMG 1 (# studies)
eGene Myers' cis & trans

Gene in Data Sources
Gene set name Method of gene set Description Info
CV:PGCnp Genome-wide Association Study GWAS
DMG:Jaffe_2016 Genome-wide DNA methylation analysis This dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 1
PMID:cooccur High-throughput literature-search Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
Literature High-throughput literature-search 与精神分裂症Co-occurance关键词:schizophrenia,schizophrenic,schizophrenias Click to show details
GO_Annotation Mapping neuro-related keywords to Gene Ontology annotations Hits with neuro-related keywords: 4

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

Probe Chromosome Position Nearest gene P (dis) Beta (dis) FDR (dis) Study
cg06559368 10 43573319 RET 3.92E-9 -0.022 2.44E-6 DMG:Jaffe_2016

@eQTL annotation

SNP ID Chromosome Position eGene Gene Entrez ID pvalue qvalue TSS distance eQTL type
rs7370564 0 RET 5979 0.17 trans

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
Gene Pearson's Correlation Spearman's Correlation
KDM2A 0.61 0.65
GON4L 0.61 0.65
UBR4 0.61 0.65
CABLES2 0.60 0.65
AGPAT6 0.60 0.64
XXbac-B461K10.1 0.60 0.66
MAP3K3 0.60 0.65
TNRC6A 0.60 0.64
TNRC6C 0.60 0.65
DIDO1 0.60 0.64
Top 10 negatively co-expressed genes
Gene Pearson's Correlation Spearman's Correlation
AF347015.31 -0.48 -0.55
MT-CO2 -0.46 -0.53
IFI27 -0.46 -0.55
HIGD1B -0.45 -0.56
B2M -0.45 -0.53
AC021016.1 -0.45 -0.56
AF347015.27 -0.45 -0.52
AF347015.21 -0.44 -0.61
COPZ2 -0.44 -0.52
C5orf53 -0.44 -0.48

Section III. Gene Ontology annotation

Molecular function GO term Evidence Neuro keywords PubMed ID
GO:0004714 transmembrane receptor protein tyrosine kinase activity IEA neurite (GO term level: 8) -
GO:0000166 nucleotide binding IEA -
GO:0004872 receptor activity IEA -
GO:0004872 receptor activity TAS 7824936
GO:0005509 calcium ion binding IEA -
GO:0005515 protein binding IEA -
GO:0005524 ATP binding IEA -
GO:0005524 ATP binding NAS -
GO:0004713 protein tyrosine kinase activity NAS -
GO:0016740 transferase activity IEA -
GO:0016301 kinase activity IEA -
Biological process GO term Evidence Neuro keywords PubMed ID
GO:0042551 neuron maturation IEA neuron (GO term level: 10) -
GO:0048484 enteric nervous system development IEA neuron (GO term level: 7) -
GO:0007399 nervous system development IEA neurite (GO term level: 5) -
GO:0000165 MAPKKK cascade IEA -
GO:0001755 neural crest cell migration IEA -
GO:0001657 ureteric bud development IEA -
GO:0001838 embryonic epithelial tube formation IEA -
GO:0007156 homophilic cell adhesion IEA -
GO:0006468 protein amino acid phosphorylation NAS -
GO:0006468 protein amino acid phosphorylation TAS 7824936
GO:0007165 signal transduction TAS 7824936
GO:0007497 posterior midgut development TAS 8114939
Cellular component GO term Evidence Neuro keywords PubMed ID
GO:0005794 Golgi apparatus IDA 18029348
GO:0005737 cytoplasm IDA 18029348
GO:0016021 integral to membrane IEA -
GO:0005886 plasma membrane IDA 18029348

Section IV. Protein-protein interaction annotation

Interactors Aliases B Official full name B Experimental Source PubMed ID
CBL C-CBL | CBL2 | RNF55 Cas-Br-M (murine) ecotropic retroviral transforming sequence - HPRD 12727845
CRK CRKII v-crk sarcoma virus CT10 oncogene homolog (avian) Reconstituted Complex BioGRID 9393871
DOK1 MGC117395 | MGC138860 | P62DOK docking protein 1, 62kDa (downstream of tyrosine kinase 1) - HPRD,BioGRID 12087092
DOK2 p56DOK | p56dok-2 docking protein 2, 56kDa - HPRD,BioGRID 11470823
DOK3 DOKL | FLJ22570 | FLJ39939 docking protein 3 - HPRD 11470823
DOK4 FLJ10488 docking protein 4 - HPRD,BioGRID 11470823
DOK5 C20orf180 | MGC16926 docking protein 5 - HPRD,BioGRID 11470823
DOK6 DOK5L | HsT3226 | MGC20785 docking protein 6 - HPRD,BioGRID 15286081
FRS2 FRS2A | FRS2alpha | SNT | SNT-1 | SNT1 fibroblast growth factor receptor substrate 2 RET interacts with FRS2 BIND 11390647
FRS2 FRS2A | FRS2alpha | SNT | SNT-1 | SNT1 fibroblast growth factor receptor substrate 2 - HPRD,BioGRID 11360177
GAB1 - GRB2-associated binding protein 1 - HPRD 11360177
GDNF ATF1 | ATF2 | HFB1-GDNF glial cell derived neurotrophic factor - HPRD 8674117|9482105
GFRA1 GDNFR | GDNFRA | GFR-ALPHA-1 | MGC23045 | RET1L | RETL1 | TRNR1 GDNF family receptor alpha 1 - HPRD 9740802|10829012
GFRA1 GDNFR | GDNFRA | GFR-ALPHA-1 | MGC23045 | RET1L | RETL1 | TRNR1 GDNF family receptor alpha 1 Reconstituted Complex BioGRID 9192898|10829012
GOLGA5 GOLIM5 | RFG5 | ret-II golgi autoantigen, golgin subfamily a, 5 - HPRD 2734021|9915833
GRB10 GRB-IR | Grb-10 | IRBP | KIAA0207 | MEG1 | RSS growth factor receptor-bound protein 10 - HPRD,BioGRID 7665556
GRB2 ASH | EGFRBP-GRB2 | Grb3-3 | MST084 | MSTP084 growth factor receptor-bound protein 2 - HPRD 9393871
GRB2 ASH | EGFRBP-GRB2 | Grb3-3 | MST084 | MSTP084 growth factor receptor-bound protein 2 Reconstituted Complex BioGRID 7665556|8183561
GRB7 - growth factor receptor-bound protein 7 - HPRD,BioGRID 8631863
NRTN NTN neurturin - HPRD,BioGRID 9192898
PDLIM7 LMP1 PDZ and LIM domain 7 (enigma) - HPRD,BioGRID 12176011
PIK3R1 GRB1 | p85 | p85-ALPHA phosphoinositide-3-kinase, regulatory subunit 1 (alpha) - HPRD 10652352
PLCG1 PLC-II | PLC1 | PLC148 | PLCgamma1 phospholipase C, gamma 1 RET9 phosphorylates PLC-gamma via its amino-terminal SH2 domain. This interaction was modelled on a demonstrated interaction between RET9 from human and PLC-gamma from cow. BIND 9047383
PLCG1 PLC-II | PLC1 | PLC148 | PLCgamma1 phospholipase C, gamma 1 - HPRD,BioGRID 8628282
PTPRF FLJ43335 | FLJ45062 | FLJ45567 | LAR protein tyrosine phosphatase, receptor type, F - HPRD,BioGRID 11121408
SHC1 FLJ26504 | SHC | SHCA SHC (Src homology 2 domain containing) transforming protein 1 RET9 phosphorylates Shc. BIND 9047383
SHC1 FLJ26504 | SHC | SHCA SHC (Src homology 2 domain containing) transforming protein 1 - HPRD,BioGRID 8183561|9047384
SRC ASV | SRC1 | c-SRC | p60-Src v-src sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog (avian) - HPRD,BioGRID 10070972
STAT3 APRF | FLJ20882 | HIES | MGC16063 signal transducer and activator of transcription 3 (acute-phase response factor) - HPRD,BioGRID 11536047|12637586
|15485908


Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
KEGG ENDOCYTOSIS 183 132 All SZGR 2.0 genes in this pathway
KEGG PATHWAYS IN CANCER 328 259 All SZGR 2.0 genes in this pathway
KEGG THYROID CANCER 29 26 All SZGR 2.0 genes in this pathway
PID RET PATHWAY 39 29 All SZGR 2.0 genes in this pathway
PID AJDISS 2PATHWAY 48 38 All SZGR 2.0 genes in this pathway
NAKAMURA CANCER MICROENVIRONMENT UP 26 14 All SZGR 2.0 genes in this pathway
GAZDA DIAMOND BLACKFAN ANEMIA ERYTHROID DN 493 298 All SZGR 2.0 genes in this pathway
SENGUPTA NASOPHARYNGEAL CARCINOMA WITH LMP1 UP 408 247 All SZGR 2.0 genes in this pathway
TURASHVILI BREAST DUCTAL CARCINOMA VS DUCTAL NORMAL UP 44 25 All SZGR 2.0 genes in this pathway
TURASHVILI BREAST DUCTAL CARCINOMA VS LOBULAR NORMAL UP 73 50 All SZGR 2.0 genes in this pathway
DOANE BREAST CANCER ESR1 UP 112 72 All SZGR 2.0 genes in this pathway
WANG LMO4 TARGETS UP 372 227 All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS 8HR DN 129 84 All SZGR 2.0 genes in this pathway
ELVIDGE HYPOXIA DN 146 94 All SZGR 2.0 genes in this pathway
ELVIDGE HYPOXIA BY DMOG DN 59 40 All SZGR 2.0 genes in this pathway
ELVIDGE HIF2A TARGETS UP 6 5 All SZGR 2.0 genes in this pathway
ELVIDGE HIF1A AND HIF2A TARGETS UP 41 22 All SZGR 2.0 genes in this pathway
GOZGIT ESR1 TARGETS DN 781 465 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
FARMER BREAST CANCER BASAL VS LULMINAL 330 215 All SZGR 2.0 genes in this pathway
LIEN BREAST CARCINOMA METAPLASTIC VS DUCTAL DN 114 58 All SZGR 2.0 genes in this pathway
LI WILMS TUMOR VS FETAL KIDNEY 2 DN 51 42 All SZGR 2.0 genes in this pathway
INGRAM SHH TARGETS DN 64 41 All SZGR 2.0 genes in this pathway
HASEGAWA TUMORIGENESIS BY RET C634R 11 7 All SZGR 2.0 genes in this pathway
GEORGES TARGETS OF MIR192 AND MIR215 893 528 All SZGR 2.0 genes in this pathway
FRASOR RESPONSE TO ESTRADIOL UP 37 28 All SZGR 2.0 genes in this pathway
STOSSI RESPONSE TO ESTRADIOL 50 35 All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 20HR UP 240 152 All SZGR 2.0 genes in this pathway
LEE AGING NEOCORTEX DN 80 49 All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 48HR UP 180 125 All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS STEM CELL AND PROGENITOR 681 420 All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 6HR UP 953 554 All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 6HR DN 911 527 All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 24HR UP 783 442 All SZGR 2.0 genes in this pathway
RIGGINS TAMOXIFEN RESISTANCE UP 66 44 All SZGR 2.0 genes in this pathway
FINETTI BREAST CANCERS KINOME BLUE 21 16 All SZGR 2.0 genes in this pathway
IWANAGA CARCINOGENESIS BY KRAS PTEN UP 181 112 All SZGR 2.0 genes in this pathway
OSADA ASCL1 TARGETS UP 46 30 All SZGR 2.0 genes in this pathway
SMID BREAST CANCER RELAPSE IN BRAIN DN 85 58 All SZGR 2.0 genes in this pathway
SMID BREAST CANCER LUMINAL B UP 172 109 All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL DN 701 446 All SZGR 2.0 genes in this pathway
CONRAD STEM CELL 39 27 All SZGR 2.0 genes in this pathway
YAUCH HEDGEHOG SIGNALING PARACRINE UP 149 85 All SZGR 2.0 genes in this pathway
GRESHOCK CANCER COPY NUMBER UP 323 240 All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP 1305 895 All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K4ME3 AND H3K27ME3 1069 729 All SZGR 2.0 genes in this pathway
VALK AML CLUSTER 16 26 17 All SZGR 2.0 genes in this pathway
VALK AML WITH 11Q23 REARRANGED 22 13 All SZGR 2.0 genes in this pathway
POOLA INVASIVE BREAST CANCER UP 288 168 All SZGR 2.0 genes in this pathway
YAGI AML WITH 11Q23 REARRANGED 351 238 All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2 AND H3K27ME3 349 234 All SZGR 2.0 genes in this pathway
STEIN ESR1 TARGETS 85 55 All SZGR 2.0 genes in this pathway
STEIN ESTROGEN RESPONSE NOT VIA ESRRA 18 12 All SZGR 2.0 genes in this pathway
BOYLAN MULTIPLE MYELOMA PCA3 UP 80 54 All SZGR 2.0 genes in this pathway
NAKAYAMA SOFT TISSUE TUMORS PCA1 DN 74 47 All SZGR 2.0 genes in this pathway
MIKKELSEN NPC HCP WITH H3K4ME3 AND H3K27ME3 210 148 All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 1HR UP 61 44 All SZGR 2.0 genes in this pathway
DUTERTRE雌二醇反应6小时 229 149 All SZGR 2.0 genes in this pathway
DUTERTRE ESTRADIOL RESPONSE 24HR UP 324 193 All SZGR 2.0 genes in this pathway
BHAT ESR1 TARGETS NOT VIA AKT1 UP 211 131 All SZGR 2.0 genes in this pathway
BHAT ESR1 TARGETS VIA AKT1 UP 281 183 All SZGR 2.0 genes in this pathway
PHONG TNF RESPONSE VIA P38 COMPLETE 227 151 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-103/107 1161 1167 m8 hsa-miR-103brain AGCAGCAUUGUACAGGGCUAUGA
hsa-miR-107brain AGCAGCAUUGUACAGGGCUAUCA
miR-128 1595 1602 1A,m8 hsa-miR-128a UCACAGUGAACCGGUCUCUUUU
hsa-miR-128b UCACAGUGAACCGGUCUCUUUC
miR-15/16/195/424/497 1162 1169 1A,m8 hsa-miR-15abrain UAGCAGCACAUAAUGGUUUGUG
hsa-miR-16brain UAGCAGCACGUAAAUAUUGGCG
hsa-miR-15bbrain UAGCAGCACAUCAUGGUUUACA
hsa-miR-195SZ UAGCAGCACAGAAAUAUUGGC
hsa-miR-424 CAGCAGCAAUUCAUGUUUUGAA
hsa-miR-497 CAGCAGCACACUGUGGUUUGU
miR-218 666 672 1A hsa-miR-218brain UUGUGCUUGAUCUAACCAUGU
hsa-miR-218brain UUGUGCUUGAUCUAACCAUGU
miR-27 1596 1602 m8 hsa-miR-27abrain UUCACAGUGGCUAAGUUCCGC
hsa-miR-27bbrain UUCACAGUGGCUAAGUUCUGC
miR-377 1116 1123 1A,m8 hsa-miR-377 AUCACACAAAGGCAACUUUUGU
miR-503 1163 1169 1A hsa-miR-503 UAGCAGCGGGAACAGUUCUGCAG