Gene Page:COL9A2
Summary?
| GeneID | 1298 |
| Symbol | COL9A2 |
| Synonyms | DJ39G22.4|EDM2|MED|STL5 |
| Description | collagen type IX alpha 2 |
| Reference | MIM:120260|HGNC:HGNC:2218|Ensembl:ENSG00000049089|HPRD:00373|Vega:OTTHUMG00000005761 |
| Gene type | protein-coding |
| Map location | 1p33-p32 |
| Pascal p-value | 0.137 |
| Fetal beta | -0.461 |
| DMG | 1 (# studies) |
| eGene | Myers' cis & trans |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:PGCnp | Genome-wide Association Study | GWAS | |
| DMG:Wockner_2014 | Genome-wide DNA methylation analysis | This 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
Differentially methylated gene| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg18186394 | 1 | 40783185 | COL9A2 | 2.08E-5 | -0.614 | 0.016 | DMG:Wockner_2014 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs2166856 | chr3 | 13268997 | COL9A2 | 1298 | 0.14 | trans | ||
| rs5003961 | chr7 | 78072443 | COL9A2 | 1298 | 0.1 | trans | ||
| rs4515471 | chr7 | 78072585 | COL9A2 | 1298 | 0.1 | trans | ||
| rs10259327 | chr7 | 78074924 | COL9A2 | 1298 | 0.1 | trans | ||
| rs7830259 | chr8 | 14087643 | COL9A2 | 1298 | 2.735E-4 | trans | ||
| rs2823906 | chr21 | 17977868 | COL9A2 | 1298 | 0.11 | trans | ||
| rs5942141 | chrX | 91433860 | COL9A2 | 1298 | 0.09 | trans |
Section II. Transcriptome annotation
General gene expression (GTEx)
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
死神:胎儿(13 - 26 postconceptionweeks), 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 | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| SHROOM1 | 0.84 | 0.81 |
| PLXNB3 | 0.83 | 0.83 |
| UAP1L1 | 0.82 | 0.82 |
| PCTK3 | 0.82 | 0.84 |
| CD22 | 0.81 | 0.81 |
| AC021593.2 | 0.81 | 0.79 |
| TMC6 | 0.81 | 0.80 |
| KIAA1755 | 0.80 | 0.76 |
| SEMA3B | 0.80 | 0.81 |
| AC024575.3 | 0.80 | 0.80 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson'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 name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| PID AVB3 INTEGRIN PATHWAY | 75 | 53 | All SZGR 2.0 genes in this pathway |
| PID SYNDECAN 1 PATHWAY | 46 | 29 | All SZGR 2.0 genes in this pathway |
| REACTOME DEVELOPMENTAL BIOLOGY | 396 | 292 | All SZGR 2.0 genes in this pathway |
| REACTOME EXTRACELLULAR MATRIX ORGANIZATION | 87 | 42 | All SZGR 2.0 genes in this pathway |
| REACTOME COLLAGEN FORMATION | 58 | 31 | All SZGR 2.0 genes in this pathway |
| REACTOME SIGNALING BY PDGF | 122 | 93 | All SZGR 2.0 genes in this pathway |
| REACTOME AXON GUIDANCE | 251 | 188 | All SZGR 2.0 genes in this pathway |
| REACTOME NCAM1 INTERACTIONS | 39 | 27 | All SZGR 2.0 genes in this pathway |
| REACTOME NCAM SIGNALING FOR NEURITE OUT GROWTH | 64 | 49 | All SZGR 2.0 genes in this pathway |
| VANHARANTA UTERINE FIBROID UP | 45 | 26 | All SZGR 2.0 genes in this pathway |
| WANG ESOPHAGUS CANCER VS NORMAL UP | 121 | 72 | All SZGR 2.0 genes in this pathway |
| LASTOWSKA NEUROBLASTOMA COPY NUMBER DN | 800 | 473 | All SZGR 2.0 genes in this pathway |
| RICKMAN HEAD AND NECK CANCER A | 100 | 63 | All SZGR 2.0 genes in this pathway |
| BENPORATH SUZ12 TARGETS | 1038 | 678 | All SZGR 2.0 genes in this pathway |
| BENPORATH EED TARGETS | 1062 | 725 | All SZGR 2.0 genes in this pathway |
| BENPORATH ES WITH H3K27ME3 | 1118 | 744 | All SZGR 2.0 genes in this pathway |
| BENPORATH PRC2 TARGETS | 652 | 441 | All SZGR 2.0 genes in this pathway |
| ROSS AML WITH MLL FUSIONS | 78 | 45 | All SZGR 2.0 genes in this pathway |
| ZHAN MULTIPLE MYELOMA LB UP | 48 | 28 | All SZGR 2.0 genes in this pathway |
| XU RESPONSE TO TRETINOIN UP | 16 | 10 | All SZGR 2.0 genes in this pathway |
| NIELSEN GIST VS SYNOVIAL SARCOMA UP | 19 | 12 | All SZGR 2.0 genes in this pathway |
| KANG CISPLATIN RESISTANCE DN | 8 | 6 | All SZGR 2.0 genes in this pathway |
| HELLER SILENCED BY METHYLATION UP | 282 | 183 | All SZGR 2.0 genes in this pathway |
| WOO LIVER CANCER RECURRENCE UP | 105 | 75 | All SZGR 2.0 genes in this pathway |
| MIKKELSEN MCV6 HCP WITH H3K27ME3 | 435 | 318 | All SZGR 2.0 genes in this pathway |
| SETLUR PROSTATE CANCER TMPRSS2 ERG FUSION UP | 67 | 48 | All SZGR 2.0 genes in this pathway |
| GUTIERREZ CHRONIC LYMPHOCYTIC LEUKEMIA DN | 56 | 39 | All SZGR 2.0 genes in this pathway |
| NIELSEN SYNOVIAL SARCOMA UP | 18 | 14 | All SZGR 2.0 genes in this pathway |
| LIM MAMMARY STEM CELL UP | 489 | 314 | All SZGR 2.0 genes in this pathway |
| ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY | 1725 | 838 | All SZGR 2.0 genes in this pathway |
| NABA胶原蛋白 | 44 | 26 | All SZGR 2.0 genes in this pathway |
| NABA CORE MATRISOME | 275 | 148 | All SZGR 2.0 genes in this pathway |
| NABA MATRISOME | 1028 | 559 | All SZGR 2.0 genes in this pathway |