Gene Page: GMDS

Summary ?
GeneID2762
SymbolGMDS
SynonymsGMD|SDR3E1
DescriptionGDP-mannose 4,6-dehydratase
ReferenceMIM:602884|HGNC:HGNC:4369|Ensembl:ENSG00000112699|HPRD:11925|Vega:OTTHUMG00000016143
Gene typeprotein-coding
Map location6p25
Pascal p-value0.361
Sherlock p-value0.852
Fetal beta-0.303
DMG3 (# studies)
eGeneMyers' cis & trans

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Jaffe_2016Genome-wide DNA methylation analysisThis dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 3
DMG:Montano_2016Genome-wide DNA methylation analysisThis dataset includes 172 replicated associations between CpGs with schizophrenia. 3
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). 3
GSMA_IGenome scan meta-analysisPsr: 0.0159 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg0631521761629850GMDS4.51E-50.0060.093DMG:Montano_2016
cg1178683961635578GMDS3.28E-60.4740.009DMG:Wockner_2014
cg0893232062246077GMDS1.07E-8-0.0154.57E-6DMG:Jaffe_2016

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs17135501chr62704474GMDS27620.15cis
rs17135521chr62707631GMDS27620.15cis
rs11706314chr345309716GMDS27620.11trans
rs2922180chr3125280472GMDS27620.01trans
rs2971271chr3125450402GMDS27620.12trans
rs2976809chr3125451738GMDS27621.767E-4trans
rs7668550chr4104384355GMDS27620trans
rs6449550chr561034312GMDS27620.13trans
rs9313797chr5158465457GMDS27620.07trans
rs17056474chr5158468105GMDS27620.07trans
rs9321275chr6131493217GMDS27620.04trans
rs2199402chr89201002GMDS27620.01trans
rs7841407chr89243427GMDS27620trans
rs2061799chr997795003GMDS27620.08trans
rs11067174chr12115011927GMDS27620.06trans
rs9529974chr1372821935GMDS27620.14trans
rs17720221chr1375182377GMDS27620.01trans
rs7165622chr1593979910GMDS27620.05trans
rs11873703chr1861448702GMDS27620.01trans
rs6095741chr2048666589GMDS27620.01trans

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
TTC160.340.23
GUCY2D0.330.23
IL28RA0.330.11
EYA20.320.26
ATBF10.310.10
KCNIP10.310.17
TSHZ20.310.14
TNFRSF11B0.310.29
ALK0.300.14
C13orf290.300.19
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
GPR22-0.25-0.29
EMX1-0.23-0.25
GTDC1-0.22-0.20
C6orf115-0.21-0.24
CIDEA-0.21-0.26
B3GALT2-0.21-0.20
AC021078.3-0.21-0.27
NEUROD6-0.21-0.24
IER5L-0.21-0.20
SEH1L-0.20-0.22

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0003824catalytic activityIEA-
GO:0005488bindingIEA-
GO:0016829lyase activityIEA-
GO:0008446GDP-mannose 4,6-dehydratase activityIEA-
GO:0008446GDP-mannose 4,6-dehydratase activityTAS11698403 
GO:0016491oxidoreductase activityIEA-
GO:0050662coenzyme bindingIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0005975carbohydrate metabolic processTAS9525924 
GO:0008152metabolic processIEA-
GO:0007159leukocyte adhesionNAS11698403 
GO:0042351'de novo' GDP-L-fucose biosynthetic processTAS11698403 
GO:0019673GDP-mannose metabolic processIEA-
GO:0044237cellular metabolic processIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005622intracellularIEA-
GO:0005737cytoplasmIC11698403 

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG FRUCTOSE AND MANNOSE METABOLISM 3423All SZGR 2.0 genes in this pathway
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM 4430All SZGR 2.0 genes in this pathway
NAKAMURA TUMOR ZONE PERIPHERAL VS CENTRAL DN 634384All SZGR 2.0 genes in this pathway
LIU PROSTATE CANCER UP 9657All SZGR 2.0 genes in this pathway
ONKEN UVEAL MELANOMA DN 526357All SZGR 2.0 genes in this pathway
CHEMNITZ RESPONSE TO PROSTAGLANDIN E2 DN 391222All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP 1382904All SZGR 2.0 genes in this pathway
DOANE RESPONSE TO ANDROGEN UP 184125All SZGR 2.0 genes in this pathway
VECCHI GASTRIC CANCER ADVANCED VS EARLY DN 13870All SZGR 2.0 genes in this pathway
WAMUNYOKOLI OVARIAN CANCER LMP UP 265158All SZGR 2.0 genes in this pathway
WAMUNYOKOLI OVARIAN CANCER GRADES 1 2 UP 13784All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA UP 1821933All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS A UP 191128All SZGR 2.0 genes in this pathway
KOYAMA SEMA3B TARGETS UP 292168All SZGR 2.0 genes in this pathway
BENPORATH MYC MAX TARGETS 775494All SZGR 2.0 genes in this pathway
AMIT EGF RESPONSE 480 HELA 164118All SZGR 2.0 genes in this pathway
PENG RAPAMYCIN RESPONSE UP 203130All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS EARLY PROGENITOR 532309All SZGR 2.0 genes in this pathway
REN ALVEOLAR RHABDOMYOSARCOMA DN 408274All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 DN 830547All SZGR 2.0 genes in this pathway
GAJATE RESPONSE TO TRABECTEDIN DN 1911All SZGR 2.0 genes in this pathway
BAELDE DIABETIC NEPHROPATHY DN 434302All 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 DN 1011592All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 3 720440All SZGR 2.0 genes in this pathway
MARSON BOUND BY FOXP3 UNSTIMULATED 1229713All SZGR 2.0 genes in this pathway
ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE UP 863514All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL UP 648398All SZGR 2.0 genes in this pathway
IZADPANAH STEM CELL ADIPOSE VS BONE UP 12692All SZGR 2.0 genes in this pathway
GRADE COLON CANCER UP 871505All SZGR 2.0 genes in this pathway
CROMER TUMORIGENESIS DN 5129All SZGR 2.0 genes in this pathway
YAGI AML WITH 11Q23 REARRANGED 351238All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC 1103714All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS CONFLUENT 567365All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 2 DN 336211All SZGR 2.0 genes in this pathway
ACEVEDO FGFR1 TARGETS IN PROSTATE CANCER MODEL UP 289184All SZGR 2.0 genes in this pathway