Gene Page: SMPD1

Summary ?
GeneID6609
SymbolSMPD1
SynonymsASM|ASMASE|NPD
Descriptionsphingomyelin phosphodiesterase 1
ReferenceMIM:607608|HGNC:HGNC:11120|Ensembl:ENSG00000166311|HPRD:06353|Vega:OTTHUMG00000165453
Gene typeprotein-coding
Map location11p15.4-p15.1
Pascal p-value0.309
Sherlock p-value0.812
Fetal beta-0.978
DMG1 (# studies)
eGeneMyers' cis & trans

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
ADT:Sun_2012Systematic Investigation of Antipsychotic Drugs and Their TargetsA total of 382 drug-target associations involving 43 antipsychotic drugs and 49 target genes.
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Wockner_2014Genome-wide DNA methylation analysisThis dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24). 1
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 1 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg17121955116411382SMPD15.146E-4-0.2220.047DMG:Wockner_2014

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs8141327chr2248747918SMPD166090.04trans

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
CLU0.770.92
GPR37L10.770.92
HLA-E0.770.90
PRODH0.760.91
SLC39A120.760.86
HEPN10.750.89
GRIN2C0.750.88
SELENBP10.750.89
TSC22D40.740.89
FAM151A0.740.87
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
DUSP12-0.63-0.82
MLLT11-0.62-0.79
PARP6-0.62-0.79
GSTA4-0.62-0.81
SUPV3L1-0.62-0.81
PPP3CC-0.62-0.79
STMN1-0.61-0.80
C9orf30-0.61-0.80
ZWILCH-0.61-0.78
SPATS2-0.61-0.79

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0004767sphingomyelin phosphodiesterase activityTAS1718266 
GO:0016798hydrolase activity, acting on glycosyl bondsIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0007399nervous system developmentTASneurite (GO term level: 5)7670466 
GO:0007165signal transductionTAS7670466 
GO:0008152metabolic processIEA-
GO:0006685sphingomyelin catabolic processIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005764lysosomeIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG SPHINGOLIPID METABOLISM 4026All SZGR 2.0 genes in this pathway
KEGG LYSOSOME 12183All SZGR 2.0 genes in this pathway
BIOCARTA CERAMIDE PATHWAY 2216All SZGR 2.0 genes in this pathway
BIOCARTA EDG1 PATHWAY 2724All SZGR 2.0 genes in this pathway
ST FAS SIGNALING PATHWAY 6554All SZGR 2.0 genes in this pathway
PID TRAIL PATHWAY 2820All SZGR 2.0 genes in this pathway
PID FAS PATHWAY 3829All SZGR 2.0 genes in this pathway
PID TNF PATHWAY 4633All SZGR 2.0 genes in this pathway
PID IL2 PI3K PATHWAY 3427All SZGR 2.0 genes in this pathway
PID CERAMIDE PATHWAY 4837All SZGR 2.0 genes in this pathway
REACTOME GLYCOSPHINGOLIPID METABOLISM 3822All SZGR 2.0 genes in this pathway
REACTOME PHOSPHOLIPID METABOLISM 198112All SZGR 2.0 genes in this pathway
REACTOME SPHINGOLIPID METABOLISM 6940All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF LIPIDS AND LIPOPROTEINS 478302All SZGR 2.0 genes in this pathway
PARENT MTOR SIGNALING UP 567375All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 1 UP 380236All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 2 UP 418263All SZGR 2.0 genes in this pathway
ENK UV RESPONSE KERATINOCYTE UP 530342All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 UP 309199All SZGR 2.0 genes in this pathway
GRUETZMANN PANCREATIC CANCER DN 203134All SZGR 2.0 genes in this pathway
NUYTTEN NIPP1 TARGETS DN 848527All SZGR 2.0 genes in this pathway
FRIDMAN SENESCENCE UP 7760All SZGR 2.0 genes in this pathway
TARTE PLASMA CELL VS PLASMABLAST UP 398262All SZGR 2.0 genes in this pathway
FRASOR RESPONSE TO ESTRADIOL DN 8252All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS 882572All SZGR 2.0 genes in this pathway
ZHAN MULTIPLE MYELOMA UP 6446All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS STEM CELL LONG TERM 302191All SZGR 2.0 genes in this pathway
MARIADASON RESPONSE TO CURCUMIN SULINDAC 5 2317All SZGR 2.0 genes in this pathway
SATO SILENCED BY METHYLATION IN PANCREATIC CANCER 1 419273All SZGR 2.0 genes in this pathway
MCCOLLUM GELDANAMYCIN RESISTANCE UP 109All SZGR 2.0 genes in this pathway
MASSARWEH TAMOXIFEN RESISTANCE UP 578341All SZGR 2.0 genes in this pathway
BERNARD PPAPDC1B TARGETS UP 4020All SZGR 2.0 genes in this pathway
MATZUK SPERMATOZOA 11477All SZGR 2.0 genes in this pathway
MOOTHA PGC 420269All SZGR 2.0 genes in this pathway
ZHANG TLX TARGETS 60HR UP 293203All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA HAPTOTAXIS DN 668419All SZGR 2.0 genes in this pathway
NAKAMURA ADIPOGENESIS LATE UP 10467All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS CONFLUENT 567365All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP B 549316All SZGR 2.0 genes in this pathway
ALFANO MYC TARGETS 239156All SZGR 2.0 genes in this pathway