Gene Page: COL9A2

Summary ?
GeneID1298
SymbolCOL9A2
SynonymsDJ39G22.4|EDM2|MED|STL5
Descriptioncollagen type IX alpha 2
ReferenceMIM:120260|HGNC:HGNC:2218|Ensembl:ENSG00000049089|HPRD:00373|Vega:OTTHUMG00000005761
Gene typeprotein-coding
Map location1p33-p32
Pascal p-value0.137
Fetal beta-0.461
DMG1 (# studies)
eGeneMyers' cis & trans

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
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

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg18186394140783185COL9A22.08E-5-0.6140.016DMG:Wockner_2014

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs2166856chr313268997COL9A212980.14trans
rs5003961chr778072443COL9A212980.1trans
rs4515471chr778072585COL9A212980.1trans
rs10259327chr778074924COL9A212980.1trans
rs7830259chr814087643COL9A212982.735E-4trans
rs2823906chr2117977868COL9A212980.11trans
rs5942141chrX91433860COL9A212980.09trans

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
SHROOM10.840.81
PLXNB30.830.83
UAP1L10.820.82
PCTK30.820.84
CD220.810.81
AC021593.20.810.79
TMC60.810.80
KIAA17550.800.76
SEMA3B0.800.81
AC024575.30.800.80
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
STMN1-0.59-0.65
STMN2-0.57-0.62
CRMP1-0.56-0.60
RNF2-0.56-0.63
MED19-0.56-0.64
TUBB2B-0.55-0.60
POLB-0.55-0.63
YBX1-0.55-0.68
ARMCX1-0.55-0.65
TUBB-0.55-0.60

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
PID AVB3 INTEGRIN PATHWAY 7553All SZGR 2.0 genes in this pathway
PID SYNDECAN 1 PATHWAY 4629All SZGR 2.0 genes in this pathway
REACTOME DEVELOPMENTAL BIOLOGY 396292All SZGR 2.0 genes in this pathway
REACTOME EXTRACELLULAR MATRIX ORGANIZATION 8742All SZGR 2.0 genes in this pathway
REACTOME COLLAGEN FORMATION 5831All SZGR 2.0 genes in this pathway
REACTOME SIGNALING BY PDGF 12293All SZGR 2.0 genes in this pathway
REACTOME AXON GUIDANCE 251188All SZGR 2.0 genes in this pathway
REACTOME NCAM1 INTERACTIONS 3927All SZGR 2.0 genes in this pathway
REACTOME NCAM SIGNALING FOR NEURITE OUT GROWTH 6449All SZGR 2.0 genes in this pathway
VANHARANTA UTERINE FIBROID UP 4526All SZGR 2.0 genes in this pathway
WANG ESOPHAGUS CANCER VS NORMAL UP 12172All SZGR 2.0 genes in this pathway
LASTOWSKA NEUROBLASTOMA COPY NUMBER DN 800473All SZGR 2.0 genes in this pathway
RICKMAN HEAD AND NECK CANCER A 10063All 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
BENPORATH ES WITH H3K27ME3 1118744All SZGR 2.0 genes in this pathway
BENPORATH PRC2 TARGETS 652441All SZGR 2.0 genes in this pathway
ROSS AML WITH MLL FUSIONS 7845All SZGR 2.0 genes in this pathway
ZHAN MULTIPLE MYELOMA LB UP 4828All SZGR 2.0 genes in this pathway
XU RESPONSE TO TRETINOIN UP 1610All SZGR 2.0 genes in this pathway
NIELSEN GIST VS SYNOVIAL SARCOMA UP 1912All SZGR 2.0 genes in this pathway
KANG CISPLATIN RESISTANCE DN 86All SZGR 2.0 genes in this pathway
HELLER SILENCED BY METHYLATION UP 282183All SZGR 2.0 genes in this pathway
WOO LIVER CANCER RECURRENCE UP 10575All SZGR 2.0 genes in this pathway
MIKKELSEN MCV6 HCP WITH H3K27ME3 435318All SZGR 2.0 genes in this pathway
SETLUR PROSTATE CANCER TMPRSS2 ERG FUSION UP 6748All SZGR 2.0 genes in this pathway
GUTIERREZ CHRONIC LYMPHOCYTIC LEUKEMIA DN 5639All SZGR 2.0 genes in this pathway
NIELSEN SYNOVIAL SARCOMA UP 1814All SZGR 2.0 genes in this pathway
LIM MAMMARY STEM CELL UP 489314All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY 1725838All SZGR 2.0 genes in this pathway
NABA COLLAGENS 4426All SZGR 2.0 genes in this pathway
NABA CORE MATRISOME 275148All SZGR 2.0 genes in this pathway
NABA MATRISOME 1028559All SZGR 2.0 genes in this pathway