Gene Page: LSM2

Summary ?
GeneID57819
SymbolLSM2
SynonymsC6orf28|G7B|YBL026W|snRNP
DescriptionLSM2 homolog, U6 small nuclear RNA and mRNA degradation associated
ReferenceMIM:607282|HGNC:HGNC:13940|Ensembl:ENSG00000204392|HPRD:06282|Vega:OTTHUMG00000031121
Gene typeprotein-coding
Map location6p21.3
Pascal p-value1E-12
Sherlock p-value0.084
Fetal beta0.574
DMG1 (# studies)
eGeneMeta

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
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). 2
GSMA_IGenome scan meta-analysisPsr: 0.033 
NetworkShortest path distance of core genes in the Human protein-protein interaction networkContribution to shortest path in PPI network: 0.1805 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg04331511631775519LSM22.05E-50.2280.016DMG:Wockner_2014
cg01937314631774612LSM21.535E-4-0.2410.032DMG:Wockner_2014


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:0003723RNA bindingIEA-
GO:0005515protein bindingIPI15231747 
GO:0017070U6 snRNA bindingNAS10523320 
GO:0019901protein kinase bindingIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0000398nuclear mRNA splicing, via spliceosomeEXP12226669 
GO:0000398nuclear mRNA splicing, via spliceosomeNAS-
GO:0008380RNA splicingIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005634nucleusNAS-
GO:0005681spliceosomeIEA-

Section IV. Protein-protein interaction annotation

InteractorsAliases BOfficial full name BExperimentalSourcePubMed ID
C14orf1ERG28 | NET51chromosome 14 open reading frame 1Two-hybridBioGRID16169070 
CRMP1DPYSL1 | DRP-1 | DRP1collapsin response mediator protein 1Two-hybridBioGRID16169070 
DDX20DKFZp434H052 | DP103 | GEMIN3DEAD (Asp-Glu-Ala-Asp) box polypeptide 20Affinity Capture-Western
Reconstituted Complex		BioGRID10601333 
GBP2-guanylate binding protein 2, interferon-inducibleTwo-hybridBioGRID16169070 
LSM1CASM | YJL124CLSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae)-HPRD,BioGRID11920408 |15231747 
LSM3SMX4 | USS2 | YLR438CLSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae)-HPRD11920408 |15231747 
LSM3SMX4 | USS2 | YLR438CLSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae)Two-hybridBioGRID14667819 |15231747 
|16169070 |16189514 
LSM4YER112WLSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae)-HPRD,BioGRID11920408 
LSM5FLJ12710 | YER146WLSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae)-HPRD11920408 
LSM6YDR378CLSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae)-HPRD11920408 
LSM7YNL147WLSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae)Two-hybridBioGRID14667819 |15231747 
LSM7YNL147WLSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae)-HPRD11920408 |15231747 
LSM8YJR022WLSM8 homolog, U6 small nuclear RNA associated (S. cerevisiae)-HPRD11920408 |15231747 
LSM8YJR022WLSM8 homolog, U6 small nuclear RNA associated (S. cerevisiae)Two-hybridBioGRID14667819 |15231747 
RSRC1BM-011 | MGC12197arginine/serine-rich coiled-coil 1Two-hybridBioGRID16169070 
SMN1BCD541 | SMA | SMA1 | SMA2 | SMA3 | SMA4 | SMA@ | SMN | SMNT | T-BCD541survival of motor neuron 1, telomeric-HPRD,BioGRID10851237 
ZBTB16PLZF | ZNF145zinc finger and BTB domain containing 16Two-hybridBioGRID16169070 
ZNF408FLJ12827zinc finger protein 408-HPRD14667819 


Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG RNA DEGRADATION 5937All SZGR 2.0 genes in this pathway
KEGG SPLICEOSOME 12872All SZGR 2.0 genes in this pathway
REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA 14077All SZGR 2.0 genes in this pathway
REACTOME MRNA PROCESSING 16186All SZGR 2.0 genes in this pathway
REACTOME MRNA SPLICING 11158All SZGR 2.0 genes in this pathway
REACTOME MRNA SPLICING MINOR PATHWAY 4519All SZGR 2.0 genes in this pathway
REACTOME MRNA DECAY BY 5 TO 3 EXORIBONUCLEASE 1510All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF MRNA 284128All SZGR 2.0 genes in this pathway
REACTOME DEADENYLATION DEPENDENT MRNA DECAY 4829All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF RNA 330155All SZGR 2.0 genes in this pathway
PRAMOONJAGO SOX4 TARGETS DN 5135All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS DN 459276All SZGR 2.0 genes in this pathway
CONCANNON APOPTOSIS BY EPOXOMICIN DN 172112All SZGR 2.0 genes in this pathway
BERENJENO TRANSFORMED BY RHOA UP 536340All SZGR 2.0 genes in this pathway
GRASEMANN RETINOBLASTOMA WITH 6P AMPLIFICATION 1414All SZGR 2.0 genes in this pathway
DIRMEIER LMP1 RESPONSE LATE DN 3222All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK 16521023All SZGR 2.0 genes in this pathway
GROSS HYPOXIA VIA ELK3 AND HIF1A DN 10371All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS DN 637377All SZGR 2.0 genes in this pathway
LE EGR2 TARGETS UP 10875All SZGR 2.0 genes in this pathway
FLECHNER PBL KIDNEY TRANSPLANT OK VS DONOR UP 151100All SZGR 2.0 genes in this pathway
SASAKI ADULT T CELL LEUKEMIA 176122All SZGR 2.0 genes in this pathway
RAMALHO STEMNESS UP 206118All SZGR 2.0 genes in this pathway
PAL PRMT5 TARGETS UP 203135All SZGR 2.0 genes in this pathway
GENTILE UV RESPONSE CLUSTER D7 4021All SZGR 2.0 genes in this pathway
GENTILE UV HIGH DOSE DN 312203All SZGR 2.0 genes in this pathway
MARSON BOUND BY E2F4 UNSTIMULATED 728415All SZGR 2.0 genes in this pathway
ZHANG TLX TARGETS 60HR DN 277166All SZGR 2.0 genes in this pathway
HAN SATB1 TARGETS UP 395249All SZGR 2.0 genes in this pathway
CHIANG LIVER CANCER SUBCLASS UNANNOTATED DN 193112All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA CLASSES UP 605377All SZGR 2.0 genes in this pathway
WONG EMBRYONIC STEM CELL CORE 335193All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS GROWING 243155All SZGR 2.0 genes in this pathway
QI HYPOXIA TARGETS OF HIF1A AND FOXA2 3727All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 DN 918550All SZGR 2.0 genes in this pathway
FEVR CTNNB1 TARGETS DN 553343All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION UP 570339All SZGR 2.0 genes in this pathway