Gene Page: PHGDH

Summary ?
GeneID26227
SymbolPHGDH
Synonyms3-PGDH|3PGDH|HEL-S-113|NLS|NLS1|PDG|PGAD|PGD|PGDH|PHGDHD|SERA
Descriptionphosphoglycerate dehydrogenase
ReferenceMIM:606879|HGNC:HGNC:8923|Ensembl:ENSG00000092621|HPRD:06047|Vega:OTTHUMG00000012100
Gene typeprotein-coding
Map location1p12
Pascal p-value0.485
Sherlock p-value0.753
Fetal beta-0.698
eGeneMyers' cis & trans
SupportCELL METABOLISM
G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS
G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL
G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS
CompositeSet

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.
GSMA_IGenome scan meta-analysisPsr: 0.0235 
GSMA_IIAGenome scan meta-analysis (All samples)Psr: 0.00814 
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophreniasClick to show details
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 1 

Section I. Genetics and epigenetics annotation

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs4501739chrX35960848PHGDH262270.03trans

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:0004617phosphoglycerate dehydrogenase activityIEA-
GO:0004617phosphoglycerate dehydrogenase activityTAS8758134 
GO:0005215transporter activityIEA-
GO:0048037cofactor bindingIEA-
GO:0009055electron carrier activityTAS8758134 
GO:0016491oxidoreductase activityIEA-
GO:0051287NAD bindingIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0007420brain developmentTASBrain (GO term level: 7)8758134 
GO:0008652amino acid biosynthetic processIEA-
GO:0006810transportIEA-
GO:0006564L-serine biosynthetic processIEA-
GO:0055114oxidation reductionIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005576extracellular regionIEA-

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
REACTOME METABOLISM OF AMINO ACIDS AND DERIVATIVES 200136All SZGR 2.0 genes in this pathway
REACTOME AMINO ACID SYNTHESIS AND INTERCONVERSION TRANSAMINATION 1714All 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 UP 285181All SZGR 2.0 genes in this pathway
GAZDA DIAMOND BLACKFAN ANEMIA PROGENITOR DN 6642All SZGR 2.0 genes in this pathway
IGARASHI ATF4 TARGETS DN 9065All SZGR 2.0 genes in this pathway
GARY CD5 TARGETS UP 473314All SZGR 2.0 genes in this pathway
SENESE HDAC3 TARGETS DN 536332All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA DN 1375806All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED UP 633376All SZGR 2.0 genes in this pathway
PACHER TARGETS OF IGF1 AND IGF2 UP 3527All SZGR 2.0 genes in this pathway
ENK UV RESPONSE EPIDERMIS DN 508354All SZGR 2.0 genes in this pathway
VANHARANTA UTERINE FIBROID WITH 7Q DELETION UP 6737All 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
HAMAI APOPTOSIS VIA TRAIL UP 584356All SZGR 2.0 genes in this pathway
KAN RESPONSE TO ARSENIC TRIOXIDE 12380All SZGR 2.0 genes in this pathway
MCBRYAN TERMINAL END BUD DN 76All SZGR 2.0 genes in this pathway
FARMER BREAST CANCER BASAL VS LULMINAL 330215All SZGR 2.0 genes in this pathway
SCHLOSSER SERUM RESPONSE DN 712443All SZGR 2.0 genes in this pathway
TERAMOTO OPN TARGETS CLUSTER 7 1916All SZGR 2.0 genes in this pathway
SHETH LIVER CANCER VS TXNIP LOSS PAM1 229137All SZGR 2.0 genes in this pathway
SHETH LIVER CANCER VS TXNIP LOSS PAM3 7037All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS DN 1024594All SZGR 2.0 genes in this pathway
RAHMAN TP53 TARGETS PHOSPHORYLATED 2118All SZGR 2.0 genes in this pathway
BENPORATH NANOG TARGETS 988594All SZGR 2.0 genes in this pathway
BENPORATH OCT4 TARGETS 290172All SZGR 2.0 genes in this pathway
MORI PRE BI LYMPHOCYTE UP 8054All SZGR 2.0 genes in this pathway
ONDER CDH1 TARGETS 1 UP 14085All SZGR 2.0 genes in this pathway
PENG LEUCINE DEPRIVATION UP 14293All SZGR 2.0 genes in this pathway
JECHLINGER EPITHELIAL TO MESENCHYMAL TRANSITION UP 7151All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS 882572All SZGR 2.0 genes in this pathway
ZHAN MULTIPLE MYELOMA CD1 UP 4529All SZGR 2.0 genes in this pathway
ZHAN MULTIPLE MYELOMA CD1 VS CD2 UP 6647All SZGR 2.0 genes in this pathway
MATSUDA NATURAL KILLER DIFFERENTIATION 475313All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS UP 3727All SZGR 2.0 genes in this pathway
KIM GASTRIC CANCER CHEMOSENSITIVITY 10364All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 UP 428266All SZGR 2.0 genes in this pathway
XU GH1 AUTOCRINE TARGETS UP 268157All 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
HOWLIN CITED1 TARGETS 2 DN 1711All 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
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
ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE DN 274165All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER WITH H3K27ME3 DN 228114All SZGR 2.0 genes in this pathway
SMID BREAST CANCER RELAPSE IN BONE DN 315197All SZGR 2.0 genes in this pathway
SMID BREAST CANCER LUMINAL B DN 564326All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL UP 648398All 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 DN 14593All SZGR 2.0 genes in this pathway
LABBE WNT3A TARGETS UP 11271All SZGR 2.0 genes in this pathway
BLUM RESPONSE TO SALIRASIB UP 245159All SZGR 2.0 genes in this pathway
MUELLER PLURINET 299189All SZGR 2.0 genes in this pathway
VANTVEER BREAST CANCER ESR1 DN 240153All SZGR 2.0 genes in this pathway
HOSHIDA LIVER CANCER LATE RECURRENCE DN 6948All SZGR 2.0 genes in this pathway
YOSHIOKA LIVER CANCER EARLY RECURRENCE DN 6531All SZGR 2.0 genes in this pathway
KARLSSON TGFB1 TARGETS UP 12778All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS SENESCENT 572352All 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
LU EZH2 TARGETS UP 295155All SZGR 2.0 genes in this pathway
LI DCP2 BOUND MRNA 8957All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN 19721213All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP D 280158All 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
FORTSCHEGGER PHF8 TARGETS UP 279155All SZGR 2.0 genes in this pathway