Gene Page: SHMT2

Summary ?
GeneID6472
SymbolSHMT2
SynonymsGLYA|HEL-S-51e|SHMT
Descriptionserine hydroxymethyltransferase 2
ReferenceMIM:138450|HGNC:HGNC:10852|Ensembl:ENSG00000182199|HPRD:00717|Vega:OTTHUMG00000171246
Gene typeprotein-coding
Map location12q12-q14
Pascal p-value0.01
Sherlock p-value0.256
Fetal beta1.023
eGeneMyers' cis & trans

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:PGC128Genome-wide Association StudyA multi-stage schizophrenia GWAS of up to 36,989 cases and 113,075 controls. Reported by the Schizophrenia Working Group of PGC. 128 independent associations spanning 108 loci
CV:PGCnpGenome-wide Association StudyGWAS

Section I. Genetics and epigenetics annotation

@CV:PGC128

SNP IDChromosomePositionAllelePFunctionGeneUp/Down Distance
rs12826178chr1257622371TG5.297E-12upstreamSHMT2

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs10943541chr679190082SHMT264720.14trans
rs1578978chr8118196802SHMT264720.13trans

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
DMWD0.840.84
CHPF0.840.85
AMPD20.840.83
STMN30.840.81
PPP2R5B0.830.81
MAPK8IP10.820.80
REEP20.820.81
ATP13A20.820.81
SYT50.820.83
LRRTM10.810.86
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
AF347015.21-0.58-0.42
AF347015.2-0.54-0.40
MT-CO2-0.53-0.39
GNG11-0.53-0.48
AF347015.8-0.53-0.39
AF347015.18-0.53-0.36
NOSTRIN-0.52-0.41
AF347015.31-0.52-0.39
AP002478.3-0.52-0.45
AF347015.33-0.51-0.38

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0005515protein bindingIPI17220478 |17353931 
GO:0004372glycine hydroxymethyltransferase activityIDA8505317 |17482557 
GO:0004372glycine hydroxymethyltransferase activityIEA-
GO:0016740transferase activityIEA-
GO:0030170pyridoxal phosphate bindingIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0006730one-carbon compound metabolic processIDA11516159 
GO:0006730one-carbon compound metabolic processIEA-
GO:0006544glycine metabolic processIEA-
GO:0006563L-serine metabolic processIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005739mitochondrionIDA17482557 
GO:0005739mitochondrionIEA-
GO:0005743mitochondrial inner membraneIEA-
GO:0005759mitochondrial matrixIDA11516159 

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG GLYCINE SERINE AND THREONINE METABOLISM 3126All SZGR 2.0 genes in this pathway
KEGG ONE CARBON POOL BY FOLATE 1712All SZGR 2.0 genes in this pathway
PARENT MTOR SIGNALING UP 567375All SZGR 2.0 genes in this pathway
NAKAMURA TUMOR ZONE PERIPHERAL VS CENTRAL DN 634384All SZGR 2.0 genes in this pathway
SOTIRIOU BREAST CANCER GRADE 1 VS 3 UP 15184All SZGR 2.0 genes in this pathway
CHEMNITZ RESPONSE TO PROSTAGLANDIN E2 UP 14686All SZGR 2.0 genes in this pathway
GARY CD5 TARGETS UP 473314All SZGR 2.0 genes in this pathway
CASORELLI ACUTE PROMYELOCYTIC LEUKEMIA DN 663425All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP 1382904All SZGR 2.0 genes in this pathway
HOEBEKE LYMPHOID STEM CELL DN 8659All SZGR 2.0 genes in this pathway
RHEIN ALL GLUCOCORTICOID THERAPY DN 362238All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS DN 459276All SZGR 2.0 genes in this pathway
GRAHAM CML DIVIDING VS NORMAL QUIESCENT UP 181101All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA DN 1375806All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA ANAPLASTIC UP 722443All SZGR 2.0 genes in this pathway
ENK UV RESPONSE EPIDERMIS UP 293179All SZGR 2.0 genes in this pathway
NADERI BREAST CANCER PROGNOSIS UP 5026All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN UP 1142669All SZGR 2.0 genes in this pathway
GRAESSMANN RESPONSE TO MC AND DOXORUBICIN UP 612367All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 UP 309199All SZGR 2.0 genes in this pathway
WANG HCP PROSTATE CANCER 11169All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK 16521023All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK 1442892All SZGR 2.0 genes in this pathway
PUJANA CHEK2 PCC NETWORK 779480All SZGR 2.0 genes in this pathway
GROSS HYPOXIA VIA HIF1A UP 7749All SZGR 2.0 genes in this pathway
CAFFAREL RESPONSE TO THC UP 3320All SZGR 2.0 genes in this pathway
CAFFAREL RESPONSE TO THC 24HR 5 DN 5935All SZGR 2.0 genes in this pathway
PENG LEUCINE DEPRIVATION UP 14293All SZGR 2.0 genes in this pathway
SMITH TERT TARGETS UP 14591All SZGR 2.0 genes in this pathway
MATSUDA NATURAL KILLER DIFFERENTIATION 475313All SZGR 2.0 genes in this pathway
BROWN MYELOID CELL DEVELOPMENT DN 12986All SZGR 2.0 genes in this pathway
LI WILMS TUMOR VS FETAL KIDNEY 1 DN 163115All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS EARLY PROGENITOR 532309All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP 16911088All SZGR 2.0 genes in this pathway
BANDRES RESPONSE TO CARMUSTIN MGMT 48HR DN 161105All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 6HR UP 953554All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 24HR UP 783442All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 1 528324All SZGR 2.0 genes in this pathway
MARSON BOUND BY FOXP3 UNSTIMULATED 1229713All SZGR 2.0 genes in this pathway
SANSOM APC TARGETS 212121All SZGR 2.0 genes in this pathway
SANSOM APC MYC TARGETS 217138All SZGR 2.0 genes in this pathway
SANSOM APC TARGETS REQUIRE MYC 210123All SZGR 2.0 genes in this pathway
HELLER SILENCED BY METHYLATION DN 10567All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS DN 292189All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS SILENCED BY METHYLATION DN 281179All SZGR 2.0 genes in this pathway
ACEVEDO NORMAL TISSUE ADJACENT TO LIVER TUMOR DN 354216All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER DN 540340All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL CULTURED VS FRESH UP 425298All SZGR 2.0 genes in this pathway
BLUM RESPONSE TO SALIRASIB UP 245159All SZGR 2.0 genes in this pathway
MOOTHA HUMAN MITODB 6 2002 429260All SZGR 2.0 genes in this pathway
MOOTHA MITOCHONDRIA 447277All SZGR 2.0 genes in this pathway
TOOKER GEMCITABINE RESISTANCE DN 12284All SZGR 2.0 genes in this pathway
BOHN PRIMARY IMMUNODEFICIENCY SYNDROM UP 4730All SZGR 2.0 genes in this pathway
ZHANG TLX TARGETS 60HR DN 277166All SZGR 2.0 genes in this pathway
KARLSSON TGFB1 TARGETS UP 12778All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS GROWING 243155All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS CONFLUENT 567365All SZGR 2.0 genes in this pathway
OHGUCHI LIVER HNF4A TARGETS DN 14985All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE EARLY LATE 317190All SZGR 2.0 genes in this pathway
VANDESLUIS COMMD1 TARGETS GROUP 3 UP 8950All SZGR 2.0 genes in this pathway
DELPUECH FOXO3 TARGETS DN 4127All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS DN 882538All SZGR 2.0 genes in this pathway
KIM TIAL1 TARGETS 3222All SZGR 2.0 genes in this pathway
HUANG GATA2 TARGETS DN 7252All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-3834985051A,m8hsa-miR-383brainAGAUCAGAAGGUGAUUGUGGCU
miR-4955475531Ahsa-miR-495brainAAACAAACAUGGUGCACUUCUUU