Gene Page: EYA3
Summary ?
| GeneID | 2140 |
| Symbol | EYA3 |
| Synonyms | - |
| Description | EYA transcriptional coactivator and phosphatase 3 |
| Reference | MIM:601655|HGNC:HGNC:3521|Ensembl:ENSG00000158161|HPRD:09042|Vega:OTTHUMG00000003916 |
| Gene type | protein-coding |
| Map location | 1p36 |
| Pascal p-value | 0.202 |
| Fetal beta | 0.772 |
| DMG | 1 (# studies) |
| eGene | Anterior cingulate cortex BA24 Cerebellar Hemisphere Cerebellum Cortex Frontal Cortex BA9 Myers' cis & trans |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:GWASdb | Genome-wide Association Studies | GWASdb records for schizophrenia | |
| 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. | 1 |
Section I. Genetics and epigenetics annotation
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg27498304 | 1 | 28415137 | EYA3 | 3.46E-9 | -0.008 | 2.27E-6 | DMG:Jaffe_2016 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs17714461 | chr19 | 51425105 | EYA3 | 2140 | 0.17 | trans | ||
| rs56302332 | 1 | 28298088 | EYA3 | ENSG00000158161.11 | 3.686E-9 | 0 | 117119 | gtex_brain_ba24 |
| rs6699701 | 1 | 28298951 | EYA3 | ENSG00000158161.11 | 6.785E-7 | 0 | 116256 | gtex_brain_ba24 |
| rs12406483 | 1 | 28301217 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 113990 | gtex_brain_ba24 |
| rs7529792 | 1 | 28306250 | EYA3 | ENSG00000158161.11 | 3.176E-7 | 0 | 108957 | gtex_brain_ba24 |
| rs57127818 | 1 | 28308676 | EYA3 | ENSG00000158161.11 | 1.789E-9 | 0 | 106531 | gtex_brain_ba24 |
| rs11247731 | 1 | 28309722 | EYA3 | ENSG00000158161.11 | 3.176E-7 | 0 | 105485 | gtex_brain_ba24 |
| rs12139137 | 1 | 28313606 | EYA3 | ENSG00000158161.11 | 6.785E-7 | 0 | 101601 | gtex_brain_ba24 |
| rs11247734 | 1 | 28313993 | EYA3 | ENSG00000158161.11 | 6.785E-7 | 0 | 101214 | gtex_brain_ba24 |
| rs11589329 | 1 | 28316764 | EYA3 | ENSG00000158161.11 | 1.659E-8 | 0 | 98443 | gtex_brain_ba24 |
| rs7549174 | 1 | 28319484 | EYA3 | ENSG00000158161.11 | 6.785E-7 | 0 | 95723 | gtex_brain_ba24 |
| rs72656578 | 1 | 28327622 | EYA3 | ENSG00000158161.11 | 2.669E-9 | 0 | 87585 | gtex_brain_ba24 |
| rs11247736 | 1 | 28328868 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 86339 | gtex_brain_ba24 |
| rs112765047 | 1 | 28329369 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 85838 | gtex_brain_ba24 |
| rs28845937 | 1 | 28329414 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 85793 | gtex_brain_ba24 |
| rs7521893 | 1 | 28329729 | EYA3 | ENSG00000158161.11 | 2.669E-9 | 0 | 85478 | gtex_brain_ba24 |
| rs7532150 | 1 | 28329929 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 85278 | gtex_brain_ba24 |
| rs60440583 | 1 | 28330397 | EYA3 | ENSG00000158161.11 | 7.338E-7 | 0 | 84810 | gtex_brain_ba24 |
| rs113825674 | 1 | 28332622 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 82585 | gtex_brain_ba24 |
| rs12137817 | 1 | 28333013 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 82194 | gtex_brain_ba24 |
| rs12140070 | 1 | 28335581 | EYA3 | ENSG00000158161.11 | 6.785E-7 | 0 | 79626 | gtex_brain_ba24 |
| rs72656588 | 1 | 28336180 | EYA3 | ENSG00000158161.11 | 1.004E-6 | 0 | 79027 | gtex_brain_ba24 |
| rs6691100 | 1 | 28339288 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 75919 | gtex_brain_ba24 |
| rs6683268 | 1 | 28339933 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 75274 | gtex_brain_ba24 |
| rs6683680 | 1 | 28340340 | EYA3 | ENSG00000158161.11 | 3.419E-8 | 0 | 74867 | gtex_brain_ba24 |
| rs6671333 | 1 | 28340649 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 74558 | gtex_brain_ba24 |
| rs6686688 | 1 | 28340934 | EYA3 | ENSG00000158161.11 | 5.353E-8 | 0 | 74273 | gtex_brain_ba24 |
| rs6674119 | 1 | 28340991 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 74216 | gtex_brain_ba24 |
| rs57378639 | 1 | 28341229 | EYA3 | ENSG00000158161.11 | 1.237E-8 | 0 | 73978 | gtex_brain_ba24 |
| rs6598918 | 1 | 28342777 | EYA3 | ENSG00000158161.11 | 3.419E-8 | 0 | 72430 | gtex_brain_ba24 |
| rs2275492 | 1 | 28343897 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 71310 | gtex_brain_ba24 |
| rs6684659 | 1 | 28344181 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 71026 | gtex_brain_ba24 |
| rs12144891 | 1 | 28344980 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 70227 | gtex_brain_ba24 |
| rs72656597 | 1 | 28347450 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 67757 | gtex_brain_ba24 |
| rs2815708 | 1 | 28347491 | EYA3 | ENSG00000158161.11 | 1.73E-6 | 0 | 67716 | gtex_brain_ba24 |
| rs11247738 | 1 | 28348723 | EYA3 | ENSG00000158161.11 | 3.556E-9 | 0 | 66484 | gtex_brain_ba24 |
| rs7551152 | 1 | 28349144 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 66063 | gtex_brain_ba24 |
| rs12144354 | 1 | 28349153 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 66054 | gtex_brain_ba24 |
| rs11581035 | 1 | 28350328 | EYA3 | ENSG00000158161.11 | 2.522E-9 | 0 | 64879 | gtex_brain_ba24 |
| rs72658306 | 1 | 28352115 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 63092 | gtex_brain_ba24 |
| rs11247739 | 1 | 28352647 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 62560 | gtex_brain_ba24 |
| rs397831397 | 1 | 28355093 | EYA3 | ENSG00000158161.11 | 2.663E-7 | 0 | 60114 | gtex_brain_ba24 |
| rs6671101 | 1 | 28355534 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 59673 | gtex_brain_ba24 |
| rs6674212 | 1 | 28356263 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 58944 | gtex_brain_ba24 |
| rs12119494 | 1 | 28358803 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 56404 | gtex_brain_ba24 |
| rs138259969 | 1 | 28360174 | EYA3 | ENSG00000158161.11 | 1.577E-6 | 0 | 55033 | gtex_brain_ba24 |
| rs141903187 | 1 | 28360177 | EYA3 | ENSG00000158161.11 | 7.633E-7 | 0 | 55030 | gtex_brain_ba24 |
| rs150628667 | 1 | 28360180 | EYA3 | ENSG00000158161.11 | 3.353E-6 | 0 | 55027 | gtex_brain_ba24 |
| rs546355 | 1 | 28364156 | EYA3 | ENSG00000158161.11 | 1.346E-6 | 0 | 51051 | gtex_brain_ba24 |
| rs4068839 | 1 | 28364597 | EYA3 | ENSG00000158161.11 | 5.652E-7 | 0 | 50610 | gtex_brain_ba24 |
| rs72658316 | 1 | 28364949 | EYA3 | ENSG00000158161.11 | 6.527E-10 | 0 | 50258 | gtex_brain_ba24 |
| rs6674937 | 1 | 28365988 | EYA3 | ENSG00000158161.11 | 2.574E-9 | 0 | 49219 | gtex_brain_ba24 |
| rs6687671 | 1 | 28366015 | EYA3 | ENSG00000158161.11 | 1.925E-8 | 0 | 49192 | gtex_brain_ba24 |
| rs140129016 | 1 | 28367365 | EYA3 | ENSG00000158161.11 | 3.415E-9 | 0 | 47842 | gtex_brain_ba24 |
| rs199526832 | 1 | 28369855 | EYA3 | ENSG00000158161.11 | 8.377E-9 | 0 | 45352 | gtex_brain_ba24 |
| rs490149 | 1 | 28371992 | EYA3 | ENSG00000158161.11 | 1.931E-8 | 0 | 43215 | gtex_brain_ba24 |
| rs7541031 | 1 | 28374815 | EYA3 | ENSG00000158161.11 | 2.576E-9 | 0 | 40392 | gtex_brain_ba24 |
| rs12130997 | 1 | 28375577 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 39630 | gtex_brain_ba24 |
| rs199618152 | 1 | 28376703 | EYA3 | ENSG00000158161.11 | 2.262E-6 | 0 | 38504 | gtex_brain_ba24 |
| rs11247741 | 1 | 28376887 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 38320 | gtex_brain_ba24 |
| rs10902684 | 1 | 28377053 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 38154 | gtex_brain_ba24 |
| rs12144272 | 1 | 28378384 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 36823 | gtex_brain_ba24 |
| rs11247742 | 1 | 28379130 | EYA3 | ENSG00000158161.11 | 6.785E-7 | 0 | 36077 | gtex_brain_ba24 |
| rs12128770 | 1 | 28379322 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 35885 | gtex_brain_ba24 |
| rs6661800 | 1 | 28380087 | EYA3 | ENSG00000158161.11 | 6.785E-7 | 0 | 35120 | gtex_brain_ba24 |
| rs11583358 | 1 | 28380109 | EYA3 | ENSG00000158161.11 | 2.585E-9 | 0 | 35098 | gtex_brain_ba24 |
| rs11584722 | 1 | 28380179 | EYA3 | ENSG00000158161.11 | 2.59E-9 | 0 | 35028 | gtex_brain_ba24 |
| rs521908 | 1 | 28382580 | EYA3 | ENSG00000158161.11 | 2.07E-8 | 0 | 32627 | gtex_brain_ba24 |
| rs35736331 | 1 | 28382831 | EYA3 | ENSG00000158161.11 | 2.794E-9 | 0 | 32376 | gtex_brain_ba24 |
| rs12406786 | 1 | 28383067 | EYA3 | ENSG00000158161.11 | 2.809E-9 | 0 | 32140 | gtex_brain_ba24 |
| rs551355 | 1 | 28383526 | EYA3 | ENSG00000158161.11 | 3.251E-6 | 0 | 31681 | gtex_brain_ba24 |
| rs11247745 | 1 | 28385723 | EYA3 | ENSG00000158161.11 | 3.063E-9 | 0 | 29484 | gtex_brain_ba24 |
| rs12137852 | 1 | 28387181 | EYA3 | ENSG00000158161.11 | 3.23E-9 | 0 | 28026 | gtex_brain_ba24 |
| rs57814301 | 1 | 28388420 | EYA3 | ENSG00000158161.11 | 3.434E-9 | 0 | 26787 | gtex_brain_ba24 |
| rs72658347 | 1 | 28389310 | EYA3 | ENSG00000158161.11 | 8.798E-7 | 0 | 25897 | gtex_brain_ba24 |
| rs11247746 | 1 | 28389994 | EYA3 | ENSG00000158161.11 | 9.033E-7 | 0 | 25213 | gtex_brain_ba24 |
| rs3753864 | 1 | 28390596 | EYA3 | ENSG00000158161.11 | 1.808E-6 | 0 | 24611 | gtex_brain_ba24 |
| rs11247747 | 1 | 28391015 | EYA3 | ENSG00000158161.11 | 4.179E-9 | 0 | 24192 | gtex_brain_ba24 |
| rs17185115 | 1 | 28394201 | EYA3 | ENSG00000158161.11 | 1.325E-8 | 0 | 21006 | gtex_brain_ba24 |
| rs11247748 | 1 | 28394751 | EYA3 | ENSG00000158161.11 | 1.141E-8 | 0 | 20456 | gtex_brain_ba24 |
| rs560958 | 1 | 28396122 | EYA3 | ENSG00000158161.11 | 6.304E-8 | 0 | 19085 | gtex_brain_ba24 |
| rs145158680 | 1 | 28397129 | EYA3 | ENSG00000158161.11 | 1.656E-8 | 0 | 18078 | gtex_brain_ba24 |
| rs9786989 | 1 | 28399616 | EYA3 | ENSG00000158161.11 | 8.378E-8 | 0 | 15591 | gtex_brain_ba24 |
| rs11807799 | 1 | 28400878 | EYA3 | ENSG00000158161.11 | 5.534E-8 | 0 | 14329 | gtex_brain_ba24 |
| rs72658361 | 1 | 28402924 | EYA3 | ENSG00000158161.11 | 1.302E-8 | 0 | 12283 | gtex_brain_ba24 |
| rs56003040 | 1 | 28404477 | EYA3 | ENSG00000158161.11 | 4.153E-6 | 0 | 10730 | gtex_brain_ba24 |
| rs12144063 | 1 | 28406047 | EYA3 | ENSG00000158161.11 | 2.471E-6 | 0 | 9160 | gtex_brain_ba24 |
| rs12144104 | 1 | 28406173 | EYA3 | ENSG00000158161.11 | 2.599E-6 | 0 | 9034 | gtex_brain_ba24 |
| rs397861754 | 1 | 28406666 | EYA3 | ENSG00000158161.11 | 1.967E-8 | 0 | 8541 | gtex_brain_ba24 |
| rs67776244 | 1 | 28410738 | EYA3 | ENSG00000158161.11 | 2.715E-6 | 0 | 4469 | gtex_brain_ba24 |
| rs200809661 | 1 | 28410743 | EYA3 | ENSG00000158161.11 | 9.866E-7 | 0 | 4464 | gtex_brain_ba24 |
| rs11588733 | 1 | 28411054 | EYA3 | ENSG00000158161.11 | 2.292E-8 | 0 | 4153 | gtex_brain_ba24 |
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 |
| PRMT8 | 0.67 | 0.71 |
| RHOBTB2 | 0.66 | 0.70 |
| SYT5 | 0.66 | 0.68 |
| PAK6 | 0.66 | 0.71 |
| SPTBN4 | 0.65 | 0.68 |
| PPP1R13B | 0.65 | 0.69 |
| MGAT5B | 0.64 | 0.72 |
| GFRA2 | 0.64 | 0.73 |
| PIP5K1C | 0.64 | 0.70 |
| MAPK13 | 0.63 | 0.69 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| AF347015.21 | -0.39 | -0.34 |
| GNG11 | -0.38 | -0.40 |
| AL139819.3 | -0.36 | -0.38 |
| AF347015.31 | -0.35 | -0.31 |
| AP002478.3 | -0.35 | -0.35 |
| MT-CO2 | -0.35 | -0.30 |
| C1orf54 | -0.34 | -0.37 |
| AF347015.8 | -0.33 | -0.28 |
| MT-CYB | -0.33 | -0.27 |
| AF347015.33 | -0.33 | -0.25 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| FULCHER INFLAMMATORY RESPONSE LECTIN VS LPS UP | 579 | 346 | All SZGR 2.0 genes in this pathway |
| GINESTIER BREAST CANCER ZNF217 AMPLIFIED DN | 335 | 193 | All SZGR 2.0 genes in this pathway |
| GAUSSMANN MLL AF4 FUSION TARGETS G UP | 238 | 135 | All SZGR 2.0 genes in this pathway |
| RIZ ERYTHROID DIFFERENTIATION APOBEC2 | 27 | 19 | All SZGR 2.0 genes in this pathway |
| MORI SMALL PRE BII LYMPHOCYTE UP | 86 | 57 | All SZGR 2.0 genes in this pathway |
| BYSTRYKH HEMATOPOIESIS STEM CELL AND BRAIN QTL TRANS | 185 | 114 | All SZGR 2.0 genes in this pathway |
| SHIPP DLBCL CURED VS FATAL UP | 39 | 22 | All SZGR 2.0 genes in this pathway |
| ZHANG BREAST CANCER PROGENITORS DN | 145 | 93 | All SZGR 2.0 genes in this pathway |
| GYORFFY MITOXANTRONE RESISTANCE | 57 | 35 | All SZGR 2.0 genes in this pathway |
| GOBERT OLIGODENDROCYTE DIFFERENTIATION DN | 1080 | 713 | All SZGR 2.0 genes in this pathway |
| GHANDHI DIRECT IRRADIATION UP | 110 | 68 | All SZGR 2.0 genes in this pathway |
| ZWANG TRANSIENTLY UP BY 1ST EGF PULSE ONLY | 1839 | 928 | All SZGR 2.0 genes in this pathway |