Gene Page: SLIT3

Summary ?
GeneID6586
SymbolSLIT3
SynonymsMEGF5|SLIL2|SLIT1|Slit-3|slit2
Descriptionslit guidance ligand 3
ReferenceMIM:603745|HGNC:HGNC:11087|Ensembl:ENSG00000184347|HPRD:04775|Vega:OTTHUMG00000130409
Gene typeprotein-coding
Map location5q35
Pascal p-value0.058
Sherlock p-value0.633
TADA p-value0.025
Fetal beta-1.546
eGeneMyers' cis & trans

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:GWASdbGenome-wide Association StudiesGWASdb records for schizophrenia
CV:PGCnpGenome-wide Association StudyGWAS
DNM:Gulsuner_2013Whole Exome Sequencing analysis155 DNMs identified by exome sequencing of quads or trios of schizophrenia individuals and their parents.
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 studies1Link to SZGene
GSMA_IIAGenome scan meta-analysis (All samples)Psr: 0.0276 
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophreniasClick to show details
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 2 

Section I. Genetics and epigenetics annotation

@DNM table

GeneChromosomePositionRefAltTranscriptAA changeMutation typeSiftCG46TraitStudy
SLIT3chr5168123347CTNM_001271946
NM_003062		p.1018C>Y
p.1011C>Y		missense
missense		SchizophreniaDNM:Gulsuner_2013

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs6555806chr5167799161SLIT365860.04cis

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
DDX390.950.89
AAAS0.950.90
RNASEH2A0.940.88
IMPDH20.940.93
TRIM280.930.94
WRAP530.930.91
SMARCB10.930.94
RALY0.930.92
MAD2L20.930.88
BAT10.930.92
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
AF347015.27-0.68-0.86
AF347015.31-0.68-0.85
C5orf53-0.68-0.75
MT-CO2-0.68-0.86
AF347015.33-0.67-0.85
MT-CYB-0.66-0.84
HLA-F-0.65-0.73
AF347015.8-0.65-0.85
AIFM3-0.65-0.72
S100B-0.64-0.78

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0005509calcium ion bindingNAS-
GO:0005515protein bindingTAS9813312 
GO:0005198structural molecule activityNAS-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0007417central nervous system developmentTASBrain (GO term level: 6)10349621 
GO:0007411axon guidanceIEAaxon (GO term level: 13)-
GO:0009887organ morphogenesisIEA-
GO:0007275multicellular organismal developmentTAS9813312 
GO:0030154cell differentiationIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005576extracellular regionIEA-
GO:0005615extracellular spaceTAS9813312 

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG AXON GUIDANCE 129103All SZGR 2.0 genes in this pathway
REACTOME DEVELOPMENTAL BIOLOGY 396292All SZGR 2.0 genes in this pathway
REACTOME AXON GUIDANCE 251188All SZGR 2.0 genes in this pathway
REACTOME NETRIN1 SIGNALING 4130All SZGR 2.0 genes in this pathway
BERTUCCI MEDULLARY VS DUCTAL BREAST CANCER DN 169118All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 MUTATED SIGNATURE 1 UP 276165All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 SIGNATURE 3 UP 341197All SZGR 2.0 genes in this pathway
CHEBOTAEV GR TARGETS UP 7762All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS A DN 9061All SZGR 2.0 genes in this pathway
BEGUM TARGETS OF PAX3 FOXO1 FUSION UP 6045All SZGR 2.0 genes in this pathway
SCHLOSSER SERUM RESPONSE DN 712443All SZGR 2.0 genes in this pathway
KOYAMA SEMA3B TARGETS DN 411249All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3 1118744All SZGR 2.0 genes in this pathway
CHANG POU5F1 TARGETS UP 1510All SZGR 2.0 genes in this pathway
SHEPARD CRUSH AND BURN MUTANT DN 185111All SZGR 2.0 genes in this pathway
KAAB HEART ATRIUM VS VENTRICLE UP 249170All SZGR 2.0 genes in this pathway
MAHAJAN RESPONSE TO IL1A DN 7657All SZGR 2.0 genes in this pathway
LINDVALL IMMORTALIZED BY TERT DN 8056All SZGR 2.0 genes in this pathway
MARTINEZ RB1 TARGETS DN 543317All SZGR 2.0 genes in this pathway
MARTINEZ TP53 TARGETS DN 593372All SZGR 2.0 genes in this pathway
MARTINEZ RB1 AND TP53 TARGETS DN 591366All SZGR 2.0 genes in this pathway
RIZKI TUMOR INVASIVENESS 3D DN 270181All SZGR 2.0 genes in this pathway
RIGGI EWING SARCOMA PROGENITOR DN 191123All SZGR 2.0 genes in this pathway
SMID BREAST CANCER NORMAL LIKE UP 476285All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL DN 701446All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL UP 260174All SZGR 2.0 genes in this pathway
TAYLOR METHYLATED IN ACUTE LYMPHOBLASTIC LEUKEMIA 7752All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS DN 366257All SZGR 2.0 genes in this pathway
HOSHIDA LIVER CANCER SURVIVAL UP 7349All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2 491319All SZGR 2.0 genes in this pathway
KARLSSON TGFB1 TARGETS DN 207139All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE LATE 1137655All SZGR 2.0 genes in this pathway
PURBEY TARGETS OF CTBP1 NOT SATB1 UP 344215All SZGR 2.0 genes in this pathway
WANG MLL TARGETS 289188All SZGR 2.0 genes in this pathway
ROLEF GLIS3 TARGETS 3729All SZGR 2.0 genes in this pathway
PEDRIOLI MIR31 TARGETS DN 418245All SZGR 2.0 genes in this pathway
LIM MAMMARY STEM CELL UP 489314All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 1ST EGF PULSE ONLY 1839928All SZGR 2.0 genes in this pathway
NABA ECM GLYCOPROTEINS 19699All SZGR 2.0 genes in this pathway
NABA CORE MATRISOME 275148All SZGR 2.0 genes in this pathway
NABA MATRISOME 1028559All SZGR 2.0 genes in this pathway