Gene Page: NTF3

Summary ?
GeneID4908
SymbolNTF3
SynonymsHDNF|NGF-2|NGF2|NT-3|NT3
Descriptionneurotrophin 3
ReferenceMIM:162660|HGNC:HGNC:8023|Ensembl:ENSG00000185652|HPRD:01219|Vega:OTTHUMG00000168649
Gene typeprotein-coding
Map location12p13
Pascal p-value0.008
Fetal beta2.551

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
AssociationA combined odds ratio method (Sun et al. 2008), association studies2Link to SZGene
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophrenics,schizophreniasClick to show details
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 9 

Section I. Genetics and epigenetics annotation


Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

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
RSAD20.850.78
OAS30.830.79
GBP10.800.77
MX20.800.71
PARP120.750.73
HLA-B0.740.66
SLC15A30.740.66
ACSL50.730.75
HLA-A0.730.57
GBP30.720.75
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
C17orf48-0.45-0.55
RBMX2-0.45-0.56
ZBED5-0.44-0.52
RBM3-0.44-0.51
MED19-0.44-0.54
ZNF821-0.44-0.49
WDR70-0.44-0.47
BLVRA-0.43-0.50
SAAL1-0.43-0.51
U2AF1-0.43-0.50

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0005165neurotrophin receptor bindingIEA-
GO:0008083growth factor activityIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0007420brain developmentIEABrain (GO term level: 7)-
GO:0007411axon guidanceIEAaxon (GO term level: 13)-
GO:0007403glial cell fate determinationIEAGlial (GO term level: 10)-
GO:0048699generation of neuronsIEAneuron, neurogenesis (GO term level: 7)-
GO:0048666neuron developmentIEAneuron (GO term level: 9)-
GO:0007274neuromuscular synaptic transmissionIEAneuron, Synap (GO term level: 7)-
GO:0048484enteric nervous system developmentIEAneuron (GO term level: 7)-
GO:0042490mechanoreceptor differentiationIEAneuron (GO term level: 9)-
GO:0043523regulation of neuron apoptosisIEAneuron (GO term level: 8)-
GO:0007267cell-cell signalingTAS2236018 
GO:0007165signal transductionTAS2236018 
GO:0008544epidermis developmentIEA-
GO:0007422peripheral nervous system developmentIEA-
GO:0021675nerve developmentIEA-
GO:0051145smooth muscle cell differentiationIEA-
GO:0045944positive regulation of transcription from RNA polymerase II promoterIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005576extracellular regionIEA-
GO:0016023cytoplasmic membrane-bounded vesicleIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG MAPK SIGNALING PATHWAY 267205All SZGR 2.0 genes in this pathway
KEGG NEUROTROPHIN SIGNALING PATHWAY 126103All SZGR 2.0 genes in this pathway
PID SHP2 PATHWAY 5846All SZGR 2.0 genes in this pathway
PID P75 NTR PATHWAY 6951All SZGR 2.0 genes in this pathway
PID TRKR PATHWAY 6248All SZGR 2.0 genes in this pathway
PID MAPK TRK PATHWAY 3431All SZGR 2.0 genes in this pathway
HATADA METHYLATED IN LUNG CANCER DN 3813All SZGR 2.0 genes in this pathway
SHIPP DLBCL CURED VS FATAL UP 3922All SZGR 2.0 genes in this pathway
KANG IMMORTALIZED BY TERT UP 8961All SZGR 2.0 genes in this pathway
AFFAR YY1 TARGETS UP 214133All SZGR 2.0 genes in this pathway
GENTILE UV RESPONSE CLUSTER D2 4130All SZGR 2.0 genes in this pathway
GENTILE UV HIGH DOSE DN 312203All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 6HR DN 160101All SZGR 2.0 genes in this pathway
LEE AGING MUSCLE UP 4533All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER WITH H3K27ME3 UP 295149All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3 UNMETHYLATED 536296All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K4ME3 AND H3K27ME3 1069729All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA CLASSES DN 210141All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE EARLY LATE 317190All SZGR 2.0 genes in this pathway
SERVITJA LIVER HNF1A TARGETS UP 13596All SZGR 2.0 genes in this pathway
LIM MAMMARY STEM CELL UP 489314All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY 1725838All SZGR 2.0 genes in this pathway
NABA SECRETED FACTORS 344197All SZGR 2.0 genes in this pathway
NABA MATRISOME ASSOCIATED 753411All SZGR 2.0 genes in this pathway
NABA MATRISOME 1028559All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-200bc/429249255m8hsa-miR-200bUAAUACUGCCUGGUAAUGAUGAC
hsa-miR-200cUAAUACUGCCGGGUAAUGAUGG
hsa-miR-429UAAUACUGUCUGGUAAAACCGU
hsa-miR-200bUAAUACUGCCUGGUAAUGAUGAC
hsa-miR-200cUAAUACUGCCGGGUAAUGAUGG
hsa-miR-429UAAUACUGUCUGGUAAAACCGU
miR-21133139m8hsa-miR-21brainUAGCUUAUCAGACUGAUGUUGA
hsa-miR-590GAGCUUAUUCAUAAAAGUGCAG
miR-221/22252591A,m8hsa-miR-221brainAGCUACAUUGUCUGCUGGGUUUC
hsa-miR-222brainAGCUACAUCUGGCUACUGGGUCUC
miR-369-3p85911Ahsa-miR-369-3pAAUAAUACAUGGUUGAUCUUU
miR-37485921A,m8hsa-miR-374UUAUAAUACAACCUGAUAAGUG
miR-41080861Ahsa-miR-410AAUAUAACACAGAUGGCCUGU
miR-4484652m8hsa-miR-448UUGCAUAUGUAGGAUGUCCCAU
miR-5391421481Ahsa-miR-539GGAGAAAUUAUCCUUGGUGUGU