Gene Page: HOXC4
Summary ?
| GeneID | 3221 |
| Symbol | HOXC4 |
| Synonyms | HOX3|HOX3E|cp19 |
| Description | homeobox C4 |
| Reference | MIM:142974|HGNC:HGNC:5126|Ensembl:ENSG00000198353|HPRD:00860|Vega:OTTHUMG00000160036 |
| Gene type | protein-coding |
| Map location | 12q13.3 |
| Pascal p-value | 0.89 |
| Fetal beta | -1.502 |
| DMG | 2 (# 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:vanEijk_2014 | Genome-wide DNA methylation analysis | This dataset includes 432 differentially methylated CpG sites corresponding to 391 unique transcripts between schizophrenia patients (n=260) and unaffected controls (n=250). | 5 |
| 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). | 5 |
Section I. Genetics and epigenetics annotation
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg21703606 | 12 | 54427884 | HOXC4;HOXC5 | 7.45E-5 | -0.339 | 0.025 | DMG:Wockner_2014 |
| cg05349837 | 12 | 54430991 | HOXC4 | 1.381E-4 | -0.425 | 0.031 | DMG:Wockner_2014 |
| cg02721000 | 12 | 54441213 | HOXC4 | 2.494E-4 | -0.175 | 0.037 | DMG:Wockner_2014 |
| cg19696083 | 12 | 54438419 | HOXC4 | 5.604E-4 | -0.482 | 0.049 | DMG:Wockner_2014 |
| cg20587394 | 12 | 54332209 | HOXC4 | 1.764E-4 | 3.976 | DMG:vanEijk_2014 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs214657 | chr12 | 47709570 | HOXC4 | 3221 | 0.14 | 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
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 |
| TOLLIP | 0.85 | 0.87 |
| SH3BP1 | 0.82 | 0.84 |
| EXTL1 | 0.82 | 0.74 |
| PPP1R3F | 0.81 | 0.83 |
| PRKAR1B | 0.81 | 0.82 |
| SYN1 | 0.81 | 0.82 |
| TYRO3 | 0.80 | 0.81 |
| MCHR1 | 0.80 | 0.82 |
| C16orf5 | 0.80 | 0.82 |
| ALDOA | 0.80 | 0.78 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| EIF5B | -0.43 | -0.48 |
| AC005921.3 | -0.42 | -0.52 |
| FAM36A | -0.42 | -0.37 |
| RBMX2 | -0.41 | -0.41 |
| FAM159B | -0.39 | -0.59 |
| AC010300.1 | -0.39 | -0.36 |
| C21orf57 | -0.38 | -0.37 |
| RP9P | -0.38 | -0.41 |
| AC011475.1 | -0.37 | -0.41 |
| C9orf46 | -0.37 | -0.38 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| MULLIGHAN NPM1 MUTATED SIGNATURE 1 DN | 126 | 86 | All SZGR 2.0 genes in this pathway |
| MULLIGHAN NPM1 MUTATED SIGNATURE 2 DN | 77 | 46 | All SZGR 2.0 genes in this pathway |
| MULLIGHAN NPM1 SIGNATURE 3 DN | 162 | 116 | All SZGR 2.0 genes in this pathway |
| FERREIRA EWINGS SARCOMA UNSTABLE VS STABLE DN | 98 | 59 | All SZGR 2.0 genes in this pathway |
| LOPEZ MBD TARGETS | 957 | 597 | 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 |
| FRASOR RESPONSE TO ESTRADIOL UP | 37 | 28 | All SZGR 2.0 genes in this pathway |
| LU IL4 SIGNALING | 94 | 56 | All SZGR 2.0 genes in this pathway |
| LEE AGING NEOCORTEX DN | 80 | 49 | All SZGR 2.0 genes in this pathway |
| BLALOCK ALZHEIMERS DISEASE INCIPIENT UP | 390 | 242 | All SZGR 2.0 genes in this pathway |
| BLALOCK ALZHEIMERS DISEASE UP | 1691 | 1088 | All SZGR 2.0 genes in this pathway |
| LEIN MEDULLA MARKERS | 81 | 48 | All SZGR 2.0 genes in this pathway |
| YOSHIMURA MAPK8 TARGETS UP | 1305 | 895 | All SZGR 2.0 genes in this pathway |
| AGUIRRE PANCREATIC CANCER COPY NUMBER DN | 238 | 145 | All SZGR 2.0 genes in this pathway |
| MEISSNER NPC HCP WITH H3K4ME3 AND H3K27ME3 | 142 | 103 | All SZGR 2.0 genes in this pathway |
| MEISSNER BRAIN HCP WITH H3K27ME3 | 269 | 159 | All SZGR 2.0 genes in this pathway |
| BOYLAN MULTIPLE MYELOMA PCA3 DN | 69 | 38 | All SZGR 2.0 genes in this pathway |
| WONG ADULT TISSUE STEM MODULE | 721 | 492 | All SZGR 2.0 genes in this pathway |
| MIKKELSEN NPC HCP WITH H3K4ME3 AND H3K27ME3 | 210 | 148 | All SZGR 2.0 genes in this pathway |
| BRUINS UVC RESPONSE VIA TP53 GROUP A | 898 | 516 | All SZGR 2.0 genes in this pathway |