Gene Page: HOXD11

Summary ?
GeneID3237
SymbolHOXD11
SynonymsHOX4|HOX4F
Descriptionhomeobox D11
ReferenceMIM:142986|HGNC:HGNC:5134|Ensembl:ENSG00000128713|HPRD:00869|Vega:OTTHUMG00000132510
Gene typeprotein-coding
Map location2q31.1
Pascal p-value0.033
Fetal beta-0.03
DMG2 (# 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. 2
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). 2

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg037822022176971820HOXD115.39E-5-0.40.022DMG:Wockner_2014
cg238953402176973275HOXD112.41E-8-0.0157.86E-6DMG:Jaffe_2016

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs7972594chr1211724913HOXD1132370.09trans
rs10491979chr1211727969HOXD1132370.09trans

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
C3orf390.840.84
COASY0.820.81
PIGT0.810.84
GRINA0.810.79
FAM73B0.810.80
AP2A10.810.78
RABGGTA0.800.77
ATG4D0.800.82
SLC27A40.800.77
ATP13A20.800.75
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
AF347015.21-0.56-0.44
AF347015.18-0.50-0.39
AF347015.8-0.47-0.37
AL139819.3-0.47-0.44
MT-CO2-0.46-0.37
AC010300.1-0.46-0.47
MT-ATP8-0.46-0.39
FAM159B-0.46-0.59
AF347015.31-0.46-0.36
AF347015.2-0.45-0.31

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
MYLLYKANGAS AMPLIFICATION HOT SPOT 25 156All SZGR 2.0 genes in this pathway
BENPORATH SUZ12 TARGETS 1038678All SZGR 2.0 genes in this pathway
BENPORATH EED TARGETS 1062725All SZGR 2.0 genes in this pathway
SHIN B CELL LYMPHOMA CLUSTER 1 1311All SZGR 2.0 genes in this pathway
KONDO PROSTATE CANCER HCP WITH H3K27ME3 9772All SZGR 2.0 genes in this pathway
GRESHOCK CANCER COPY NUMBER UP 323240All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K27ME3 269159All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2 AND H3K27ME3 349234All SZGR 2.0 genes in this pathway
MIKKELSEN MCV6 HCP WITH H3K27ME3 435318All SZGR 2.0 genes in this pathway
FONTAINE PAPILLARY THYROID CARCINOMA DN 8053All SZGR 2.0 genes in this pathway
MIKKELSEN NPC HCP WITH H3K27ME3 341243All SZGR 2.0 genes in this pathway
VANDESLUIS COMMD1 TARGETS GROUP 4 DN 1611All SZGR 2.0 genes in this pathway
KOINUMA TARGETS OF SMAD2 OR SMAD3 824528All SZGR 2.0 genes in this pathway
KATSANOU ELAVL1 TARGETS DN 14888All SZGR 2.0 genes in this pathway