Gene Page: NEFM

Summary ?
GeneID4741
SymbolNEFM
SynonymsNEF3|NF-M|NFM
Descriptionneurofilament, medium polypeptide
ReferenceMIM:162250|HGNC:HGNC:7734|Ensembl:ENSG00000104722|HPRD:01205|Vega:OTTHUMG00000131990
Gene typeprotein-coding
Map location8p21
Pascal p-value0.577
Sherlock p-value0.791
Fetal beta-1.791
SupportSTRUCTURAL PLASTICITY
G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS
G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL
G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS
G2Cdb.humanNRC
CompositeSet

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:GWAScatGenome-wide Association StudiesThis data set includes 560 SNPs associated with schizophrenia. A total of 486 genes were mapped to these SNPs within 50kb.
CV:PGCnpGenome-wide Association StudyGWAS
GSMA_IGenome scan meta-analysisPsr: 0.031 
GSMA_IIEGenome scan meta-analysis (European-ancestry samples)Psr: 0.00057 
GSMA_IIAGenome scan meta-analysis (All samples)Psr: 0.03086 
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 5 
NetworkShortest path distance of core genes in the Human protein-protein interaction networkContribution to shortest path in PPI network: 0.0523 

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.

No co-expressed genes in brain regions


Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0005198structural molecule activityIEA-
GO:0005200structural constituent of cytoskeletonTAS3608989 
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0031133regulation of axon diameterIEAaxon (GO term level: 14)-
GO:0008088axon cargo transportIEAaxon (GO term level: 8)-
GO:0000226microtubule cytoskeleton organizationIEA-
GO:0045110intermediate filament bundle assemblyIEA-
GO:0060052neurofilament cytoskeleton organizationIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0031594neuromuscular junctionIEAneuron, axon, Synap, Neurotransmitter (GO term level: 3)-
GO:0005883neurofilamentIEAneuron, axon (GO term level: 11)-
GO:0005883neurofilamentTASneuron, axon (GO term level: 11)3608989 
GO:0030424axonTASneuron, axon, Neurotransmitter (GO term level: 6)14662745 

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG AMYOTROPHIC LATERAL SCLEROSIS ALS 5343All SZGR 2.0 genes in this pathway
DAVICIONI PAX FOXO1 SIGNATURE IN ARMS DN 2015All SZGR 2.0 genes in this pathway
KIM RESPONSE TO TSA AND DECITABINE UP 12973All SZGR 2.0 genes in this pathway
DAVICIONI TARGETS OF PAX FOXO1 FUSIONS DN 6849All SZGR 2.0 genes in this pathway
LEE NEURAL CREST STEM CELL UP 14699All SZGR 2.0 genes in this pathway
ENK UV RESPONSE KERATINOCYTE UP 530342All SZGR 2.0 genes in this pathway
KIM MYC AMPLIFICATION TARGETS UP 201127All SZGR 2.0 genes in this pathway
HATADA METHYLATED IN LUNG CANCER UP 390236All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 12HR DN 5745All SZGR 2.0 genes in this pathway
RICKMAN HEAD AND NECK CANCER C 11347All SZGR 2.0 genes in this pathway
BENPORATH OCT4 TARGETS 290172All SZGR 2.0 genes in this pathway
BENPORATH SUZ12 TARGETS 1038678All SZGR 2.0 genes in this pathway
BENPORATH EED TARGETS 1062725All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3 1118744All SZGR 2.0 genes in this pathway
BENPORATH PRC2 TARGETS 652441All SZGR 2.0 genes in this pathway
BENPORATH MYC TARGETS WITH EBOX 230156All SZGR 2.0 genes in this pathway
FERNANDEZ BOUND BY MYC 182116All SZGR 2.0 genes in this pathway
SMITH TERT TARGETS DN 8769All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS 882572All SZGR 2.0 genes in this pathway
BASSO CD40 SIGNALING UP 10176All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 16HR UP 225139All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN 1237837All SZGR 2.0 genes in this pathway
MCCLUNG DELTA FOSB TARGETS 2WK 4836All SZGR 2.0 genes in this pathway
DAZARD RESPONSE TO UV NHEK UP 244151All SZGR 2.0 genes in this pathway
MCCLUNG CREB1 TARGETS UP 10072All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 12HR UP 11168All SZGR 2.0 genes in this pathway
DAZARD UV RESPONSE CLUSTER G2 3018All SZGR 2.0 genes in this pathway
IWANAGA CARCINOGENESIS BY KRAS PTEN UP 181112All SZGR 2.0 genes in this pathway
ACEVEDO METHYLATED IN LIVER CANCER DN 940425All SZGR 2.0 genes in this pathway
MALONEY RESPONSE TO 17AAG UP 4126All SZGR 2.0 genes in this pathway
WANG TUMOR INVASIVENESS UP 374247All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME3 AND H3K27ME3 142103All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC 1103714All SZGR 2.0 genes in this pathway
MIKKELSEN NPC HCP WITH H3K4ME3 AND H3K27ME3 210148All SZGR 2.0 genes in this pathway
DAZARD UV RESPONSE CLUSTER G24 2819All SZGR 2.0 genes in this pathway
MARTENS TRETINOIN RESPONSE UP 857456All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP D 280158All SZGR 2.0 genes in this pathway
YANG BCL3 TARGETS UP 364236All SZGR 2.0 genes in this pathway
GHANDHI DIRECT IRRADIATION UP 11068All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
let-7/983533591Ahsa-let-7abrainUGAGGUAGUAGGUUGUAUAGUU
hsa-let-7bbrainUGAGGUAGUAGGUUGUGUGGUU
hsa-let-7cbrainUGAGGUAGUAGGUUGUAUGGUU
hsa-let-7dbrainAGAGGUAGUAGGUUGCAUAGU
hsa-let-7ebrainUGAGGUAGGAGGUUGUAUAGU
hsa-let-7fbrainUGAGGUAGUAGAUUGUAUAGUU
hsa-miR-98brainUGAGGUAGUAAGUUGUAUUGUU
hsa-let-7gSZUGAGGUAGUAGUUUGUACAGU
hsa-let-7ibrainUGAGGUAGUAGUUUGUGCUGU
miR-124.13203261Ahsa-miR-124aUUAAGGCACGCGGUGAAUGCCA
miR-125/351144150m8hsa-miR-125bbrainUCCCUGAGACCCUAACUUGUGA
hsa-miR-125abrainUCCCUGAGACCCUUUAACCUGUG
miR-13525321A,m8hsa-miR-135aUAUGGCUUUUUAUUCCUAUGUGA
hsa-miR-135bUAUGGCUUUUCAUUCCUAUGUG
miR-1503893951Ahsa-miR-150UCUCCCAACCCUUGUACCAGUG
miR-242852921A,m8hsa-miR-24SZUGGCUCAGUUCAGCAGGAACAG
miR-25/32/92/363/3671171241A,m8hsa-miR-25brainCAUUGCACUUGUCUCGGUCUGA
hsa-miR-32UAUUGCACAUUACUAAGUUGC
hsa-miR-92UAUUGCACUUGUCCCGGCCUG
hsa-miR-367AAUUGCACUUUAGCAAUGGUGA
hsa-miR-92bSZUAUUGCACUCGUCCCGGCCUC