Gene Page: NEFL

Summary ?
GeneID4747
SymbolNEFL
SynonymsCMT1F|CMT2E|NF-L|NF68|NFL|PPP1R110
Descriptionneurofilament, light polypeptide
ReferenceMIM:162280|HGNC:HGNC:7739|Ensembl:ENSG00000277586|HPRD:01206|Vega:OTTHUMG00000134284
Gene typeprotein-coding
Map location8p21
Pascal p-value0.652
Sherlock p-value0.912
Fetal beta-3.908
DMG1 (# studies)
eGeneCerebellum
SupportSTRUCTURAL PLASTICITY
G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS
G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL
G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS
G2Cdb.human_TAP-PSD-95-CORE
G2Cdb.humanNRC

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Jaffe_2016Genome-wide DNA methylation analysisThis dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 2
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
GSMA_IGenome scan meta-analysisPsr: 0.031 
GSMA_IIAGenome scan meta-analysis (All samples)Psr: 0.03086 
GSMA_IIEGenome scan meta-analysis (European-ancestry samples)Psr: 0.00057 
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: 5 
NetworkShortest path distance of core genes in the Human protein-protein interaction networkContribution to shortest path in PPI network: 0.0086 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg24000873824813653NEFL1.27E-10-0.0114.83E-7DMG:Jaffe_2016
cg03533519824857567NEFL9.08E-8-0.0182.07E-5DMG:Jaffe_2016


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
IL17RA0.670.67
DLC10.660.67
INPP5D0.650.69
RUNX10.640.55
SLC41A10.640.72
SNTB10.640.67
SCN4B0.640.56
TRIM250.640.72
ITPRIPL20.630.72
EYA10.620.47
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
RPL31-0.29-0.50
ST20-0.28-0.45
RP9P-0.27-0.45
NR2C2AP-0.27-0.31
RPS3AP47-0.27-0.45
PFDN5-0.27-0.47
ZNF32-0.27-0.42
RPL27-0.27-0.44
RPL34-0.26-0.49
RPS7-0.26-0.42

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0005198structural molecule activityIEA-
GO:0005200structural constituent of cytoskeletonIDA12432080 
GO:0008022protein C-terminus bindingIPI12226091 
GO:0042802identical protein bindingIPI12432080 
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0008090retrograde axon cargo transportIMPaxon (GO term level: 9)15857389 
GO:0008089anterograde axon cargo transportIMPaxon (GO term level: 9)15857389 
GO:0019896axon transport of mitochondrionIMPaxon (GO term level: 9)15857389 
GO:0033693neurofilament bundle assemblyIDA12432080 
GO:0033693neurofilament bundle assemblyIMP15857389 
GO:0045109intermediate filament organizationIMP12432080 |17052987 
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005883neurofilamentIDAneuron, axon (GO term level: 11)15857389 
GO:0030424axonIDAneuron, axon, Neurotransmitter (GO term level: 6)14662745 
GO:0005882intermediate filamentIEA-
GO:0033596TSC1-TSC2 complexIDA12226091 

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
REACTOME TRANSMISSION ACROSS CHEMICAL SYNAPSES 186155All SZGR 2.0 genes in this pathway
REACTOME NEURONAL SYSTEM 279221All SZGR 2.0 genes in this pathway
REACTOME NEUROTRANSMITTER RECEPTOR BINDING AND DOWNSTREAM TRANSMISSION IN THE POSTSYNAPTIC CELL 137110All SZGR 2.0 genes in this pathway
REACTOME RAS ACTIVATION UOPN CA2 INFUX THROUGH NMDA RECEPTOR 1715All SZGR 2.0 genes in this pathway
REACTOME ACTIVATION OF NMDA RECEPTOR UPON GLUTAMATE BINDING AND POSTSYNAPTIC EVENTS 3732All SZGR 2.0 genes in this pathway
REACTOME CREB PHOSPHORYLATION THROUGH THE ACTIVATION OF RAS 2723All SZGR 2.0 genes in this pathway
REACTOME POST NMDA RECEPTOR ACTIVATION EVENTS 3328All SZGR 2.0 genes in this pathway
REACTOME UNBLOCKING OF NMDA RECEPTOR GLUTAMATE BINDING AND ACTIVATION 1514All SZGR 2.0 genes in this pathway
REACTOME CREB PHOSPHORYLATION THROUGH THE ACTIVATION OF CAMKII 1514All SZGR 2.0 genes in this pathway
KIM RESPONSE TO TSA AND DECITABINE UP 12973All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE LIVE UP 485293All SZGR 2.0 genes in this pathway
PEPPER CHRONIC LYMPHOCYTIC LEUKEMIA DN 218All SZGR 2.0 genes in this pathway
SENESE HDAC2 TARGETS DN 13377All SZGR 2.0 genes in this pathway
SENESE HDAC3 TARGETS UP 501327All SZGR 2.0 genes in this pathway
LEE NEURAL CREST STEM CELL UP 14699All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE FIMA UP 544308All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE LPS UP 431237All SZGR 2.0 genes in this pathway
KERLEY RESPONSE TO CISPLATIN UP 4430All SZGR 2.0 genes in this pathway
JOHANSSON GLIOMAGENESIS BY PDGFB DN 2116All SZGR 2.0 genes in this pathway
LUCAS HNF4A TARGETS DN 88All 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
KIM MYC AMPLIFICATION TARGETS UP 201127All SZGR 2.0 genes in this pathway
KIM MYCL1 AMPLIFICATION TARGETS UP 1311All SZGR 2.0 genes in this pathway
HATADA METHYLATED IN LUNG CANCER UP 390236All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS DN 1024594All 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
KANNAN TP53 TARGETS UP 5840All 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
BROWNE HCMV INFECTION 20HR UP 240152All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN 1237837All SZGR 2.0 genes in this pathway
APRELIKOVA BRCA1 TARGETS 4933All SZGR 2.0 genes in this pathway
JIANG HYPOXIA NORMAL 311205All SZGR 2.0 genes in this pathway
BILD E2F3 ONCOGENIC SIGNATURE 246153All SZGR 2.0 genes in this pathway
LEIN NEURON MARKERS 6945All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS UP 317208All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS SILENCED BY METHYLATION UP 461298All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP 1305895All SZGR 2.0 genes in this pathway
HSIAO HOUSEKEEPING GENES 389245All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME3 AND H3K27ME3 142103All SZGR 2.0 genes in this pathway
MIKKELSEN NPC HCP WITH H3K4ME3 AND H3K27ME3 210148All SZGR 2.0 genes in this pathway
WANG METASTASIS OF BREAST CANCER ESR1 DN 3018All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS CALB1 CORR UP 548370All SZGR 2.0 genes in this pathway
PASINI SUZ12 TARGETS DN 315215All SZGR 2.0 genes in this pathway
AZARE NEOPLASTIC TRANSFORMATION BY STAT3 UP 12170All SZGR 2.0 genes in this pathway
SERVITJA ISLET HNF1A TARGETS UP 163111All SZGR 2.0 genes in this pathway
YANG BCL3 TARGETS UP 364236All SZGR 2.0 genes in this pathway
KRIEG HYPOXIA NOT VIA KDM3A 770480All SZGR 2.0 genes in this pathway
RAO BOUND BY SALL4 227149All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-183182618331A,m8hsa-miR-183UAUGGCACUGGUAGAAUUCACUG
miR-1885885941Ahsa-miR-188CAUCCCUUGCAUGGUGGAGGGU
miR-192/21545511Ahsa-miR-192CUGACCUAUGAAUUGACAGCC
hsa-miR-215AUGACCUAUGAAUUGACAGAC
miR-2241301361Ahsa-miR-224CAAGUCACUAGUGGUUCCGUUUA
miR-232642711A,m8hsa-miR-23abrainAUCACAUUGCCAGGGAUUUCC
hsa-miR-23bbrainAUCACAUUGCCAGGGAUUACC
miR-25/32/92/363/3673974041A,m8hsa-miR-25brainCAUUGCACUUGUCUCGGUCUGA
hsa-miR-32UAUUGCACAUUACUAAGUUGC
hsa-miR-92UAUUGCACUUGUCCCGGCCUG
hsa-miR-367AAUUGCACUUUAGCAAUGGUGA
hsa-miR-92bSZUAUUGCACUCGUCCCGGCCUC
miR-30-5p2812881A,m8hsa-miR-30a-5pUGUAAACAUCCUCGACUGGAAG
hsa-miR-30cbrainUGUAAACAUCCUACACUCUCAGC
hsa-miR-30dSZUGUAAACAUCCCCGACUGGAAG
hsa-miR-30bSZUGUAAACAUCCUACACUCAGCU
hsa-miR-30e-5pUGUAAACAUCCUUGACUGGA
miR-3232642701Ahsa-miR-323brainGCACAUUACACGGUCGACCUCU
miR-380-5p4753m8hsa-miR-380-5pUGGUUGACCAUAGAACAUGCGC
hsa-miR-563AGGUUGACAUACGUUUCCC
miR-452104910561A,m8hsa-miR-452UGUUUGCAGAGGAAACUGAGAC