Gene Page: HOXC13
Summary ?
| GeneID | 3229 |
| Symbol | HOXC13 |
| Synonyms | ECTD9|HOX3|HOX3G |
| Description | homeobox C13 |
| Reference | MIM:142976|HGNC:HGNC:5125|Ensembl:ENSG00000123364|HPRD:00862|Vega:OTTHUMG00000160008 |
| Gene type | protein-coding |
| Map location | 12q13.3 |
| Pascal p-value | 0.425 |
| DMG | 1 (# studies) |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:PGCnp | Genome-wide Association Study | GWAS | |
| DMG:Jaffe_2016 | Genome-wide DNA methylation analysis | This dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. | 2 |
Section I. Genetics and epigenetics annotation
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg04727865 | 12 | 54331892 | HOXC13 | 3.53E-8 | -0.02 | 1.03E-5 | DMG:Jaffe_2016 |
| cg25671500 | 12 | 54332624 | HOXC13 | 6.18E-8 | -0.019 | 1.54E-5 | DMG:Jaffe_2016 |
Section II. Transcriptome annotation
General gene expression (GTEx)
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 | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| CMTM5 | 0.91 | 0.91 |
| MOG | 0.90 | 0.91 |
| DBNDD2 | 0.90 | 0.90 |
| PLA2G16 | 0.90 | 0.92 |
| RNASE1 | 0.89 | 0.90 |
| ELOVL1 | 0.89 | 0.89 |
| TMC6 | 0.89 | 0.90 |
| GJB1 | 0.89 | 0.92 |
| PLLP | 0.88 | 0.89 |
| MAL | 0.88 | 0.91 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| NKIRAS2 | -0.61 | -0.73 |
| PURG | -0.60 | -0.72 |
| CRMP1 | -0.59 | -0.75 |
| PCDHB18 | -0.59 | -0.76 |
| SMAD1 | -0.58 | -0.73 |
| GSTA4 | -0.58 | -0.75 |
| ACVR2A | -0.58 | -0.74 |
| ZBTB8A | -0.58 | -0.73 |
| STMN1 | -0.58 | -0.74 |
| HN1 | -0.58 | -0.74 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| UDAYAKUMAR MED1 TARGETS DN | 240 | 171 | All SZGR 2.0 genes in this pathway |
| GOZGIT ESR1 TARGETS DN | 781 | 465 | All SZGR 2.0 genes in this pathway |
| PEREZ TP53 TARGETS | 1174 | 695 | All SZGR 2.0 genes in this pathway |
| MYLLYKANGAS AMPLIFICATION HOT SPOT 21 | 9 | 5 | 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 |
| SHIN B CELL LYMPHOMA CLUSTER 2 | 30 | 23 | All SZGR 2.0 genes in this pathway |
| SATO SILENCED BY METHYLATION IN PANCREATIC CANCER 1 | 419 | 273 | All SZGR 2.0 genes in this pathway |
| MASSARWEH TAMOXIFEN RESISTANCE UP | 578 | 341 | All SZGR 2.0 genes in this pathway |
| SARRIO EPITHELIAL MESENCHYMAL TRANSITION UP | 180 | 114 | All SZGR 2.0 genes in this pathway |
| GRESHOCK CANCER COPY NUMBER UP | 323 | 240 | All SZGR 2.0 genes in this pathway |
| MCMURRAY TP53 HRAS COOPERATION RESPONSE DN | 67 | 46 | All SZGR 2.0 genes in this pathway |
| MEISSNER NPC HCP WITH H3K27ME3 | 79 | 59 | All SZGR 2.0 genes in this pathway |
| MEISSNER BRAIN HCP WITH H3K27ME3 | 269 | 159 | All SZGR 2.0 genes in this pathway |
| MIKKELSEN NPC HCP WITH H3K27ME3 | 341 | 243 | All SZGR 2.0 genes in this pathway |
| MIKKELSEN MEF HCP WITH H3K27ME3 | 590 | 403 | All SZGR 2.0 genes in this pathway |
| MARTENS TRETINOIN RESPONSE UP | 857 | 456 | All SZGR 2.0 genes in this pathway |
| DUTERTRE ESTRADIOL RESPONSE 24HR DN | 505 | 328 | All SZGR 2.0 genes in this pathway |
| WANG MLL TARGETS | 289 | 188 | All SZGR 2.0 genes in this pathway |
| ZWANG CLASS 2 TRANSIENTLY INDUCED BY EGF | 51 | 29 | All SZGR 2.0 genes in this pathway |