Gene Page: HLA-DMB

Summary ?
GeneID3109
SymbolHLA-DMB
SynonymsD6S221E|RING7
Descriptionmajor histocompatibility complex, class II, DM beta
ReferenceMIM:142856|HGNC:HGNC:4935|Ensembl:ENSG00000242574|HPRD:00831|Vega:OTTHUMG00000031176
Gene typeprotein-coding
Map location6p21.3
Pascal p-value7.979E-7
Sherlock p-value0.131
Fetal beta-1.992
DMG1 (# studies)
eGeneCerebellar Hemisphere
Cerebellum
Cortex
Frontal Cortex BA9
Myers' cis & trans
Meta

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:GWASdbGenome-wide Association StudiesGWASdb records for schizophrenia
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). 1
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: 0.033 
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophreniasClick to show details

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg16300030632908980HLA-DMB5.171E-4-0.7490.047DMG:Wockner_2014

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs17111364chr1097901813HLA-DMB31090.15trans
rs2707051chr1777097085HLA-DMB31090.06trans

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
HLA-DRB10.860.91
CD740.790.83
AMPD30.720.80
CR392039.30.710.77
GPR1410.700.62
ZNF4880.700.67
ZNF8310.700.69
SLC7A140.690.52
SUSD50.680.70
PHF150.680.69
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
KIAA1949-0.48-0.57
TUBB2B-0.48-0.63
NKIRAS2-0.47-0.54
ALKBH2-0.47-0.63
TRIM16L-0.47-0.59
TRAF4-0.47-0.63
TRNAU1AP-0.46-0.59
SH3BP2-0.46-0.61
ZNF311-0.46-0.60
EXOSC8-0.46-0.64

Section III. Gene Ontology annotation

Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0002504antigen processing and presentation of peptide or polysaccharide antigen via MHC class IIIEA-
GO:0006955immune responseIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005765lysosomal membraneIEA-
GO:0005768endosomeIEA-
GO:0016020membraneIEA-
GO:0016021integral to membraneIEA-
GO:0005886plasma membraneEXP11048639 |11827988 |15489916 
|17652306 
GO:0042613MHC class II protein complexIEA-
GO:0031902late endosome membraneIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG CELL ADHESION MOLECULES CAMS 13493All SZGR 2.0 genes in this pathway
KEGG ANTIGEN PROCESSING AND PRESENTATION 8965All SZGR 2.0 genes in this pathway
KEGG INTESTINAL IMMUNE NETWORK FOR IGA PRODUCTION 4836All SZGR 2.0 genes in this pathway
KEGG TYPE I DIABETES MELLITUS 4438All SZGR 2.0 genes in this pathway
KEGG LEISHMANIA INFECTION 7256All SZGR 2.0 genes in this pathway
KEGG ASTHMA 3025All SZGR 2.0 genes in this pathway
KEGG AUTOIMMUNE THYROID DISEASE 5349All SZGR 2.0 genes in this pathway
KEGG SYSTEMIC LUPUS ERYTHEMATOSUS 140100All SZGR 2.0 genes in this pathway
KEGG ALLOGRAFT REJECTION 3834All SZGR 2.0 genes in this pathway
KEGG GRAFT VERSUS HOST DISEASE 4231All SZGR 2.0 genes in this pathway
KEGG VIRAL MYOCARDITIS 7358All SZGR 2.0 genes in this pathway
REACTOME MHC CLASS II ANTIGEN PRESENTATION 9161All SZGR 2.0 genes in this pathway
REACTOME IMMUNE SYSTEM 933616All SZGR 2.0 genes in this pathway
REACTOME ADAPTIVE IMMUNE SYSTEM 539350All SZGR 2.0 genes in this pathway
SCHUETZ BREAST CANCER DUCTAL INVASIVE UP 351230All SZGR 2.0 genes in this pathway
FULCHER INFLAMMATORY RESPONSE LECTIN VS LPS DN 463290All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA DN 11679All SZGR 2.0 genes in this pathway
GRAHAM CML QUIESCENT VS NORMAL QUIESCENT DN 4732All SZGR 2.0 genes in this pathway
KOINUMA COLON CANCER MSI UP 1611All SZGR 2.0 genes in this pathway
PEREZ TP53 TARGETS 1174695All SZGR 2.0 genes in this pathway
LIANG HEMATOPOIESIS STEM CELL NUMBER LARGE VS TINY UP 4424All SZGR 2.0 genes in this pathway
MORI LARGE PRE BII LYMPHOCYTE DN 5839All SZGR 2.0 genes in this pathway
MORI IMMATURE B LYMPHOCYTE UP 5335All SZGR 2.0 genes in this pathway
MORI MATURE B LYMPHOCYTE UP 9062All SZGR 2.0 genes in this pathway
ROZANOV MMP14 TARGETS UP 266171All SZGR 2.0 genes in this pathway
ROSS ACUTE MYELOID LEUKEMIA CBF 8257All SZGR 2.0 genes in this pathway
KLEIN PRIMARY EFFUSION LYMPHOMA DN 5842All SZGR 2.0 genes in this pathway
TARTE PLASMA CELL VS B LYMPHOCYTE DN 3825All SZGR 2.0 genes in this pathway
WIELAND UP BY HBV INFECTION 10166All SZGR 2.0 genes in this pathway
SANSOM APC TARGETS DN 366238All SZGR 2.0 genes in this pathway
YU MYC TARGETS DN 5538All SZGR 2.0 genes in this pathway
MOREAUX MULTIPLE MYELOMA BY TACI UP 412249All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS LATE PROGENITOR 544307All SZGR 2.0 genes in this pathway
MCLACHLAN DENTAL CARIES DN 245144All SZGR 2.0 genes in this pathway
MCLACHLAN DENTAL CARIES UP 253147All SZGR 2.0 genes in this pathway
TUOMISTO TUMOR SUPPRESSION BY COL13A1 UP 189All SZGR 2.0 genes in this pathway
HELLER SILENCED BY METHYLATION UP 282183All SZGR 2.0 genes in this pathway
GAURNIER PSMD4 TARGETS 7355All SZGR 2.0 genes in this pathway
BEIER GLIOMA STEM CELL DN 6642All SZGR 2.0 genes in this pathway
ICHIBA GRAFT VERSUS HOST DISEASE D7 UP 10767All SZGR 2.0 genes in this pathway
ICHIBA GRAFT VERSUS HOST DISEASE 35D UP 13179All SZGR 2.0 genes in this pathway
LINDSTEDT DENDRITIC CELL MATURATION D 6844All SZGR 2.0 genes in this pathway
WUNDER INFLAMMATORY RESPONSE AND CHOLESTEROL UP 5838All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS UP 491316All SZGR 2.0 genes in this pathway
CHEN METABOLIC SYNDROM NETWORK 1210725All SZGR 2.0 genes in this pathway
POOLA INVASIVE BREAST CANCER UP 288168All SZGR 2.0 genes in this pathway
YAGI AML WITH T 8 21 TRANSLOCATION 368247All SZGR 2.0 genes in this pathway
KIM GLIS2 TARGETS UP 8461All SZGR 2.0 genes in this pathway
FEVR CTNNB1 TARGETS UP 682433All SZGR 2.0 genes in this pathway