Gene Page: SHMT1

Summary ?
GeneID6470
SymbolSHMT1
SynonymsCSHMT|SHMT
Descriptionserine hydroxymethyltransferase 1 (soluble)
ReferenceMIM:182144|HGNC:HGNC:10850|Ensembl:ENSG00000176974|HPRD:01643|Vega:OTTHUMG00000059094
Gene typeprotein-coding
Map location17p11.2
Pascal p-value0.151
Sherlock p-value0.767
Fetal beta0.164
eGeneAnterior cingulate cortex BA24
Cerebellar Hemisphere
Cerebellum
Meta

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenics,schizophreniasClick to show details

Section I. Genetics and epigenetics annotation

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs2019274391718272447SHMT1ENSG00000176974.134.42563E-60.04-5591gtex_brain_ba24
rs124529871718272449SHMT1ENSG00000176974.134.57561E-60.04-5593gtex_brain_ba24

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
PREX20.890.84
SLC4A40.880.80
TLR40.850.78
LRP40.840.81
KCNJ100.840.80
PPARA0.830.75
ATP1A20.810.81
ATP13A40.810.67
ACSS30.800.73
SASH10.800.80
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
MED19-0.42-0.61
POLB-0.39-0.61
DUSP12-0.38-0.54
ING4-0.38-0.56
DCTPP1-0.38-0.55
TRNAU1AP-0.38-0.59
NR2C2AP-0.37-0.58
DALRD3-0.37-0.61
SCNM1-0.37-0.63
TCTEX1D2-0.37-0.66

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
PID MYC ACTIV PATHWAY 7962All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF VITAMINS AND COFACTORS 5136All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF AMINO ACIDS AND DERIVATIVES 200136All SZGR 2.0 genes in this pathway
HOLLMANN APOPTOSIS VIA CD40 UP 201125All SZGR 2.0 genes in this pathway
CHEMNITZ RESPONSE TO PROSTAGLANDIN E2 DN 391222All SZGR 2.0 genes in this pathway
WILCOX RESPONSE TO PROGESTERONE UP 15290All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP 1382904All SZGR 2.0 genes in this pathway
HORIUCHI WTAP TARGETS DN 310188All SZGR 2.0 genes in this pathway
KINSEY TARGETS OF EWSR1 FLII FUSION UP 1278748All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 3 UP 329196All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY SERUM DEPRIVATION UP 552347All SZGR 2.0 genes in this pathway
BERENJENO TRANSFORMED BY RHOA UP 536340All SZGR 2.0 genes in this pathway
MISSIAGLIA REGULATED BY METHYLATION DN 12267All SZGR 2.0 genes in this pathway
WANG ESOPHAGUS CANCER VS NORMAL DN 10166All SZGR 2.0 genes in this pathway
RASHI RESPONSE TO IONIZING RADIATION 5 14789All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 UP 309199All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS DN 1024594All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS DN 637377All SZGR 2.0 genes in this pathway
WEI MYCN TARGETS WITH E BOX 795478All SZGR 2.0 genes in this pathway
MORI EMU MYC LYMPHOMA BY ONSET TIME UP 11069All SZGR 2.0 genes in this pathway
SHEPARD CRUSH AND BURN MUTANT UP 197110All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT REJECTED VS OK DN 546351All SZGR 2.0 genes in this pathway
HSIAO LIVER SPECIFIC GENES 244154All SZGR 2.0 genes in this pathway
ZHAN MULTIPLE MYELOMA MF UP 4727All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS EARLY PROGENITOR 532309All SZGR 2.0 genes in this pathway
DEBIASI APOPTOSIS BY REOVIRUS INFECTION DN 287208All SZGR 2.0 genes in this pathway
MARSON BOUND BY E2F4 UNSTIMULATED 728415All 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
MARTINEZ RB1 TARGETS UP 673430All 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
CAMPS COLON CANCER COPY NUMBER UP 9245All 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
TOYOTA TARGETS OF MIR34B AND MIR34C 463262All SZGR 2.0 genes in this pathway
ZHANG BREAST CANCER PROGENITORS UP 425253All SZGR 2.0 genes in this pathway
BLUM RESPONSE TO SALIRASIB DN 342220All SZGR 2.0 genes in this pathway
MOOTHA HUMAN MITODB 6 2002 429260All SZGR 2.0 genes in this pathway
MOOTHA PGC 420269All SZGR 2.0 genes in this pathway
BOYLAN MULTIPLE MYELOMA C D UP 13995All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS UP 491316All SZGR 2.0 genes in this pathway
ZHANG TLX TARGETS 36HR DN 185116All SZGR 2.0 genes in this pathway
ZHANG TLX TARGETS 60HR DN 277166All SZGR 2.0 genes in this pathway
ZHANG TLX TARGETS DN 8950All SZGR 2.0 genes in this pathway
HOSHIDA LIVER CANCER SUBCLASS S3 266180All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA DN 267160All SZGR 2.0 genes in this pathway
DANG REGULATED BY MYC UP 7253All SZGR 2.0 genes in this pathway
DANG MYC TARGETS UP 143100All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC 1103714All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS DN 882538All SZGR 2.0 genes in this pathway
FEVR CTNNB1 TARGETS DN 553343All SZGR 2.0 genes in this pathway
TORCHIA TARGETS OF EWSR1 FLI1 FUSION DN 321200All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION UP 570339All SZGR 2.0 genes in this pathway
KATSANOU ELAVL1 TARGETS DN 14888All SZGR 2.0 genes in this pathway
LIM MAMMARY STEM CELL DN 428246All SZGR 2.0 genes in this pathway